gentoo resync : 30.09.2020

5 files changed, 233 insertions, 39 deletions

diff --git a/sci-mathematics/4ti2/4ti2-1.6.5.ebuild b/sci-mathematics/4ti2/4ti2-1.6.5.ebuild
deleted file mode 100644
index 65d55399c3ff..000000000000
--- a/sci-mathematics/4ti2/4ti2-1.6.5.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-# The swig subdir is not used, so we can skip running autotools in it. #518000
-AT_NO_RECURSIVE=1
-
-inherit autotools-utils toolchain-funcs
-
-DESCRIPTION="Software package for algebraic, geometric and combinatorial problems"
-HOMEPAGE="http://www.4ti2.de/"
-SRC_URI="http://4ti2.de/version_${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x86-macos"
-IUSE="static-libs"
-
-DEPEND="
-	sci-mathematics/glpk:0[gmp]
-	dev-libs/gmp[cxx]"
-RDEPEND="${DEPEND}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.3.2-gold.patch
-	)
-
-src_prepare() {
-	sed \
-		-e "s:^CXX.*$:CXX=$(tc-getCXX):g" \
-		-i m4/glpk-check.m4 || die
-	autotools-utils_src_prepare
-}
diff --git a/sci-mathematics/4ti2/Manifest b/sci-mathematics/4ti2/Manifest
index b87a20d55b8a..ef1bb8ba2806 100644
--- a/sci-mathematics/4ti2/Manifest
+++ b/sci-mathematics/4ti2/Manifest
@@ -1,10 +1,8 @@
 AUX 4ti2-1.3.2-gold.patch 652 BLAKE2B a3b47b440f9417d883df52356e58267b096a273ddd725c29e97a969eb3e2281edc8ecd9342bfc1a187464b4d476c22dc095ca8060f433cd2c793c22e5a181ae0 SHA512 60b14d7b287b69adbce420f37dad5d83ce21bfa4329ea0810c67f054d35a71f6795b0a8206b268ec9cfa08f796a4cd80a34d816c691e8e3e77adcbc5217b43a7
 DIST 4ti2-1.6.2.tar.gz 5531651 BLAKE2B 1e55f8e0df242a6eeff3b66f2a4a0f6508fc5fb722ec86558c289d6c8d295b169b60c9b3172f7e672f9fc341e767221138819c6534aba9695aa43ecbf61e1ab3 SHA512 ff68f767b8677ce0ce94cca39fa3ef87835d77a951f0ec6ae28ab171bf09ae25c551d88c2cdf5bf3115b33bd32366b063533a1c22576130a00f542f9370bcd7b
-DIST 4ti2-1.6.5.tar.gz 5640117 BLAKE2B e520aebae93b7001f2d03e3e6c515e4a29a7e5e154d1a571f0a25fab26fdab9185991821a8ccf7a23e4262cf488c0ec749c9ad344535374d85c946a4d28befb3 SHA512 90dc105d99659e3c2213b484b6d21e877d7484ca0ad0373ece066df26de7c0e0cce614faaae9f7b678d03fa54f987fe95ab6d3f958477b1294a2dc00733a3a08
 DIST 4ti2-1.6.6.tar.gz 5640126 BLAKE2B e52fdfd9b406b86236795b1ba2494d9686f3c93961359bf409ddcdfeb0067e3b0904473b66268315795c8941ba0cb93dbe5e4c3cea402379bd07ee65a1951e5d SHA512 89f36aaf3d8f41bb31b37b44a013ea966d9664880473ad0d6d1825ffb00afec1eff3139c09ac6b684f0679e2ae0d201a84396bb721aa1f63dc1deca592392c41
 DIST 4ti2-1.6.7.tar.gz 5649869 BLAKE2B ab0e7da1de88e5e99ead0b8fa7f7a72773b84ae903a31dc3134e83364ea45069889f8ce9812bb471cf72b824fe013756d557489b4d2ab31216141d5b6347acfc SHA512 38d638fe01ff3cef1aebae1eefd276cf02f808978851b4465e132f77d3ab34ea51d512e2ea28a42ac65263b458c43cf420dc5f8ac930f959dd0c14916cef9841
 EBUILD 4ti2-1.6.2.ebuild 802 BLAKE2B bb6601a9e4671482ae29517090aa55cc7cd422215878be64544d0b3579ae90971464c71f676a90597c8678a56e168138af4dfbf5932876feadcc20b8f1a9aa32 SHA512 8a1aac8b45e81957f1b978e46d7ea43ee35f288a7c0f2431de1fb12883669461a517f186db68102b69d209ee1b1d5c7ab04f5bdbe74d7e71f557632c43ede56c
-EBUILD 4ti2-1.6.5.ebuild 804 BLAKE2B a98953ced8d45c1c85728048679c12a694812e77baf73802a7aaf79e8ace135b3f699be6c7775e01cf05d5c11a1969380dc462400351fb3de014aa0d0b12662e SHA512 add5b056849f4f570bcbc6c97e2802e30a5348a17721a55df19f01ca376cbd8621b721828d25c3c657f8e4f88979003cf9a54ed0adc2da04bb7a52dc52e2268d
 EBUILD 4ti2-1.6.6.ebuild 811 BLAKE2B 9371af59dc290a7e19879a97815b8fd7480fefc0c85bbc6e4af227fb303d5812392b0cdb3e5da01816cd9a98c916f0bd899fda127563a9d91e892bdef9818f5d SHA512 532ff6e560ae88d772740f7393f7eb418de3c16f0069b1d7a4bb4153fdf00a8672eb3e8f6a288184fd14b7b159c31dd87a4039f89cec065d4e61b3a0d880c297
 EBUILD 4ti2-1.6.7.ebuild 919 BLAKE2B 8b6ea74353bcc05727bc856566e16b37e22f7816c90507f441662ae18777a893deb5d44e3999a5da54dfda1c38557d91c909f4baee3e4b044a0b89dc15380178 SHA512 8c79cd88808064e58b2a6440f919a43b89b68db9a3ff96357168ccae0c2f9e62d620cef1f1441c9edcf06394923a280ae2beca425bbd7c6c78b2893bed13946f
 MISC metadata.xml 446 BLAKE2B ce737e287f6b8f420aee86ca0ce72aa4952474a3ba717239dc8d10261038faddbc9b06f93a04bc8f8c48b36606254780865bbc5038564d4fb9252241e45a7a4b SHA512 2c7950b353c54597eebcff1f50e5045f792ef37cfe59f0142160bdf5ea47ff6be57bd698b051e6c56863b109fde983c1aeeca87827289abde96838af1aa3f7d1
diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index 7975e72f352f..d4a782a20533 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index a637da34bf58..82251821778a 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -25,9 +25,11 @@ DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18
 DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
 DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
 DIST rstudio-1.3.1056.tar.gz 89584544 BLAKE2B 0e758ad97f9faa2d3932a49dafd92bc21199a5c0a20e2d8480267ebbb7cd11dc38596b4bb697e04add7bfe6b126f7b2ae6675040a0ac8caca5a5cf737f5ad6eb SHA512 8a9077c2ae021e0cf4cca41b374a50534087b35fd2c1e4b18bdd5ba3672e1ab275046e483ec8a3aba729a8e39f961149fb03a053ea005d8a32873b51201baca2
+DIST rstudio-1.3.1093.tar.gz 89554292 BLAKE2B defd68e65a2cbc570aaf6fb14bd16342946154cda7322549d426281aea48d923803f061c1cd7d74b65b000a67ed62713dd06d311617e54130cb7c08147b34694 SHA512 c8a8d2312353e574dc2fb8ff2e64bd46c8aaf889c86f9c81ce22a7275e4cbec436dadfdaee513c3fc47dd3ad003e07a25baac4d8fcf47cc21df919afa084e92e
 DIST rstudio-1.3.959.tar.gz 89639419 BLAKE2B d45b2c1b0e426ddb5a945e59a8127ddfd47f6230ef0929639c4b525382ae57437a273df6ade85cfbf3a29911cf0158ee2e0808bfa94e783d70d4615f6c228f31 SHA512 e5d8bfe16011790ff4723c731043f44070d8fe48f85c5a9ab8389c9a2b7a1d3813e9362063ec4c6a6ca3b0a0857e2190481cbb74191650a129c0d2e10b342fac
 EBUILD rstudio-1.2.5033.ebuild 7256 BLAKE2B 5b6481bbe0d02d6751ab19df0ac2a12e8d71399cb13999d65f1c6b0ce2fab49eb0ad7e55b458933d6c3fc2490f2ecc2a5e4e0c5b41c7e36a978bf825bc27f8c5 SHA512 14a307c42c979fb18c19ccf0bb68322d9382dba785421120c21c77aac666b0517e069cb60f408baa53c349c1f3b6f8ab2a59db442ec377a244ce462b395ddb1c
 EBUILD rstudio-1.2.5042.ebuild 7256 BLAKE2B 24303ced907ff45ff66fbab6638f7bda958849ae977e0b3f37e00eb396b7ff6169ae7e10b2285c804e9cec2131cce8d45bfa8197096774fef06fc859460c5aad SHA512 f5c36843edbd62a80891b1a148081e163254fcdbdc94aafd4c9051992d63704dc360c0ee129ba92b9cc0a63e39c8cf6be258606db3b1a8831f1ee8a7110ad08c
 EBUILD rstudio-1.3.1056.ebuild 7067 BLAKE2B 3e9c18d653602ad25aaa3dfd9bfbdeb34260bfe4464559c9a8ade653e5487f89d0cf043549ae212c68542f6e1fa53fab14a733f1175189af81c9daf0e019906c SHA512 e5450ef5bb210f02f7250bfb21492f94c9a694f5e59e23fe3437da91f18d34d7036de6b64cb7ef14d61f771ee18fe311b421b8dc8204b44c87356fb35f5d5263
+EBUILD rstudio-1.3.1093.ebuild 6980 BLAKE2B 51467f99af427ab86437818788918cdeec384de97b450ea7028ad046edbe259984d3e8158ae86b51e238e4d47bcd9ddef5e110532f3544bc28e6c06a3e64ca83 SHA512 9dd2ac83e838def156fb9fac7c94ccb61fae52f7144acfd924f328077dd0630a455a914dd0c59ff186878ee4ed8f4502296d07f867be2e6003a5f5a6953a4498
 EBUILD rstudio-1.3.959.ebuild 7047 BLAKE2B 78861c03e1b7aff68ba63cc00503e09eca8d67b77df12161f8bed33d226440fc70e76b584cfb4a6236836250791d6d50f127c57c9ffc36add95866db7b19ca5e SHA512 0ae6d91439d4fb22eb27d9e58d9d5bf05f6cb063e947f4431593f9cb5c60b85e9e817cd668cb1a5d8313d74ed6cb6f0136ef370a45ef4da7f1f17a9e7c8ba0ca
 MISC metadata.xml 590 BLAKE2B 53dc62775e118c9c26ee05e20ee1da1ac31b6a6b74cf7dac410856fe4e0cce40fbb800c7a03e60f59e14442baf3aad866ad42616ad5fbb5724f7f6d8c1636eea SHA512 7111442aaa52da1e554c34f824113ec0e227798dd11b0ea9148b81e7a31c08b2a527b9995e3adb9363c7a4f2a8594f30cbd4a179545bf31d69f07d5558c20f52
diff --git a/sci-mathematics/rstudio/rstudio-1.3.1093.ebuild b/sci-mathematics/rstudio/rstudio-1.3.1093.ebuild
new file mode 100644
index 000000000000..af87bd08951d
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.3.1093.ebuild
@@ -0,0 +1,231 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils cmake pam xdg-utils java-pkg-2 java-ant-2 pax-utils prefix qmake-utils vcs-clean
+
+# TODO
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+GIN_VER=2.1.2
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+PANDOC_VER=2.9.2.1
+# grep -5 QT_CANDIDATES src/cpp/desktop/CMakeLists.txt
+QT_VER=5.12.6
+QT_SLOT=5
+
+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 -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-java/aopalliance:1
+	dev-java/gin:2.1
+	dev-java/javax-inject
+	=dev-java/validation-api-1.0*:1.0[source]
+	dev-haskell/pandoc-citeproc
+	dev-lang/R
+	dev-libs/boost:=
+	>=dev-libs/mathjax-2.7.4
+	sys-apps/util-linux
+	sys-devel/clang:*
+	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/qtwebengine-${QT_VER}:${QT_SLOT}[widgets]
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( sys-libs/pam )
+	)
+	dedicated? ( sys-libs/pam )
+	dedicated? (
+		sys-libs/pam
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	server? (
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	!libressl? ( dev-libs/openssl:0= )
+	libressl? ( dev-libs/libressl:0= )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.3.959-prefs.patch
+	"${FILESDIR}"/${PN}-1.3.959-paths.patch
+	"${FILESDIR}"/${PN}-1.3.959-pandoc-mathjax.patch
+	"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
+	"${FILESDIR}"/${PN}-1.3.959-qtsingleapplication.patch
+	"${FILESDIR}"/${PN}-1.0.44-systemd.patch
+	"${FILESDIR}"/${PN}-1.3.959-core.patch
+	"${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+	"${FILESDIR}"/${PN}-1.3.1056-R-4.0.0.patch
+	"${FILESDIR}"/${PN}-1.3.1056-boost-1.74.0.patch
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	cd "${S}" || die
+	mkdir -p dependencies/common/dictionaries
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${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
+
+	# install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes
+	sed -i \
+		-e "s@\(DESTINATION \"\)\(extras/themes\"\)@\1${EROOT}/etc/rstudio/\2@" \
+		src/cpp/server/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${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 "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS aee44535570639672cf61c0545113e7a62c90b5b@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+
+	eprefixify src/gwt/build.xml
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		-DRSTUDIO_USE_SYSTEM_BOOST=TRUE
+		)
+
+	if use !dedicated; then
+		mycmakeargs+=(
+			-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+			-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		)
+	fi
+	cmake_src_configure
+}
+
+src_compile() {
+	local JAVA_ANT_REWRITE_CLASSPATH="yes"
+	local EANT_BUILD_XML="src/gwt/build.xml"
+	local EANT_BUILD_TARGET="clean"
+	java-pkg-2_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=${T}"
+	cmake_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake_src_install
+	use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}