Merge updates from master

3 files changed, 325 insertions, 0 deletions

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 728e003ec65f..5d4b2fdc3699 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -20,6 +20,7 @@ DIST rstudio-1.0.136.tar.gz 17786389 SHA256 bb6a8aa475e09dd090cd2b5ea505f578d270
 DIST rstudio-1.0.143.tar.gz 17791067 SHA256 8ae88731b4474e5e2ff9030aa14e168903fe3a7ffc4fa716f497084a86801062 SHA512 46eaa88dd8332f18bb3a43de6e262d8a365860d9add78aea6a2d345784b239972c9c73bf0b56f1736b2981b8f688dbaf5a83c6848d170c0cf61d0e51dd636a82 WHIRLPOOL db1c11be240db3528e46d359c7d40d64068dfe5f7d915c4a6b690444f7f7fbc11f3898a6e262fa625bfab906f0cbfb2a8e3288a4fd20470423a99d992972fcda
 DIST rstudio-1.0.153.tar.gz 17790922 SHA256 79b90e21e56b114e28b03fd8543a208c55bb9d5f47a87fd29143d08b9a06f7a0 SHA512 d970a9bde88845e3fc6cdaff5233ffb65c03939c685c3fca0dd052246e065c7580b3f9bc4e053a79d2ecbb5f8c283d3fce7b97cc69e43176bd49587c736dab86 WHIRLPOOL c1f4c7bdc8e5a85af53411a35d736278b83f4732d2e273378fecc77cb075dff507147d56012682564edd58041c91cc051189eb38a7348d0827b76c7ac37bd54d
 DIST rstudio-1.0.44.tar.gz 17774065 SHA256 43ece6cfdd1a13ac0e17f2a50154a30a1a14ad6c1b3cf381cc6007988ce44a0f SHA512 a8b975dc517125a257e5f61db5bb137e133b02d738d55553770aa65e388cd112ce646b53b77dc069d1ca95ccd95979f4a57ad60b99fc3b91543cf61e737e8169 WHIRLPOOL 4ad472aed130451e81d8d8e3251d3bbd701a8b8e2fbddf17dc357f39335e33c75505f9443c2c7208e60a19c2767b9328134433e5d4fd22504813020712c658ef
+DIST rstudio-1.1.368.tar.gz 20197144 SHA256 586573707a488b5f528680b932ba5f8ea6d07667cc5ae6426104e2abf5ddab75 SHA512 39cdf583d7dcd22338916cc0ea4f90681580e41663b2d3e04b2e650759c6b030c85ee111cdfe1f717f931932a9b7ca423a21585d69a785f056f754f6d50399a1 WHIRLPOOL e18ff21823638d458179819e0b0b234b80be2f095f5b7bf5b9ac0190b078f0d7acb51e8896cbfcf1ce33cd203ed4e9fbe097aac6eee62515cace1d2f08c08219
 DIST selenium-java-2.37.0.zip 24625928 SHA256 0eebba65d8edb01c1f46e462907c58f5d6e1cb0ddf63660a9985c8432bdffbb7 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779 WHIRLPOOL eb6659aae26f3c78b6f998546b23d0636c9d00ed8a7f985db1463ac4bd483ccb3e643d84e2ca0f59e0636a8de79eb552ff1d68eb6f9c06907029f7552d8f7777
 DIST selenium-server-standalone-2.37.0.jar 34730734 SHA256 97bc8c699037fb6e99ba7af570fb60dbb1b7ce30cde2448287a44ef65b13023e SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018 WHIRLPOOL 20640591534f31f24825a9ed139589b182e8b60d86541bf0be104d3cc0280983f6566bd0459f2253ac3875b48a2798b205bac8f815a119fff6db625ce9bbc29e
 DIST shinyapps-0.98.1000.tar.gz 910095 SHA256 b95c512ae0a0fb4335878d9cfcf9073e2cb3ccfed73543abe27ea8878ed36d57 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c WHIRLPOOL ecc2bce78387cb42e9989163d8fca29220e66f085acde3323417058aebb624dafa8c0e1873c7d79e67324cbd5aad250ef9fcdbbc8f659d64482233b95d898a15
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
new file mode 100644
index 000000000000..28b0220912a0
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
@@ -0,0 +1,76 @@
+Index: rstudio-1.1.357/src/cpp/session/CMakeLists.txt
+===================================================================
+--- rstudio-1.1.357.orig/src/cpp/session/CMakeLists.txt
++++ rstudio-1.1.357/src/cpp/session/CMakeLists.txt
+@@ -25,9 +25,6 @@ endif()
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
+   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # we often install embedded versions of these packages but don't do so currently
+ 
+@@ -38,22 +35,6 @@ endif()
+ #   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
+ # endif()
+ 
+-# verify libclang is installed
+-if(WIN32)
+-   set(LIBCLANG_VERSION "3.4")
+-else()
+-   set(LIBCLANG_VERSION "3.5")
+-endif()
+-set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
+-if(NOT EXISTS "${LIBCLANG_DIR}")
+-  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
+-endif()
+-set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
+-if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
+-  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
+-endif()
+-
+-
+ # include files
+ file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
+ 
+@@ -465,13 +446,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
+    install(DIRECTORY "resources/connections"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install pandoc
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.19.2.1")
+-   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}
+@@ -502,24 +476,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
+    install(DIRECTORY "resources/profiler"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install libclang
+-   if(WIN32)
+-      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_32_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
+-      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_64_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
+-   else()
+-      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
+-   endif()
+-
+-   # install libclang builtin-headers
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
+-
+    # install winpty on windows
+    if(WIN32)
+       install(PROGRAMS "${WINPTY_BINDIR_32}/winpty.dll"
diff --git a/sci-mathematics/rstudio/rstudio-1.1.368.ebuild b/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
new file mode 100644
index 000000000000..38ac6d8ddf2f
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
@@ -0,0 +1,248 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
+PANDOC_VER=1.13.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+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 -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.0
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	default
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# 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-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${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@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v0.99.903
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(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/${PN}
+		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}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 || { xdg_desktop_database_update
+		xdg_mimeinfo_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 || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+}