gentoo resync : 06.08.2019

author: V3n3RiX <venerix@redcorelinux.org> 2019-09-06 10:28:05 +0100
committer: V3n3RiX <venerix@redcorelinux.org> 2019-09-06 10:28:05 +0100
commit: f1af93971b7490792d8541bc790e0d8c6d787059 (patch)
tree: a38046712bbc3a3844d77452d16c84e716caa3d4 /sci-mathematics
parent: fc637fb28da700da71ec2064d65ca5a7a31b9c6c (diff)
32 files changed, 1775 insertions, 643 deletions
diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index 8ca02e4bcd69..468edbdc7835 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/drgeo/Manifest b/sci-mathematics/drgeo/Manifest
deleted file mode 100644
index f78b77f660e0..000000000000
--- a/sci-mathematics/drgeo/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX drgeo-1.1.0-gcc45.patch 1111 BLAKE2B 4ce022b48d3baa7fd617b560c1248d021d48e2b00491c238ec03e8c5b169a31bb271d8267ca4c818deac6cc2f45405bce1e037d5b43537fa0a467d361c701f19 SHA512 8a30d6a1e7f11194bfeb04938de594eb81bc89420102b0920f7b3e34d666a36557de5edd2cec064d7383db105c17131247c810753c7f2ee674e7f7b0b28dfa28
-DIST drgeo-1.1.0.tar.gz 1608361 BLAKE2B b7c89fb5010f7e140f891c839a0ca66fa77f47814ce15097ce7e4781faeef4d2b2269a2c5b722af0d04be76adb8b1724c252387d35d382182bc27f327143be99 SHA512 6dee654e674d76e9725ddb4c8b4374c34c93a8cd367ff827f1a8816168a85cabb6341a9b8770659e15f26d3888181b0c13e9d92ee2290df664fda55bed625f6d
-DIST drgeo-doc-1.5.tar.gz 2730242 BLAKE2B fd7b0ec0c3468a1258db47fe78476661b09d49a53d3f68314c97c60d80883a638bb7515dee02191a777eee93b90b5071ab4ecba3279949b61db05832fbb3d165 SHA512 a8010eaca8e5f8aec365317aaec277a61579f217510ffe6c0585371f139f891041388437765d6e67c3373bc87267b864f159067e142f55396a782dec9a61ff54
-EBUILD drgeo-1.1.0-r1.ebuild 1092 BLAKE2B ae9e8a404bf1c1aee434963d1b25cf5facca6fece36e4dad044ca9c550e7f749ac9bfc70762be8bea5d1974cb256b28dd07638877f302a02ceaef02c649415f7 SHA512 4a3659e64216547dc7a8c2764285184d9e68a20cd0db4cbcffa528387dd8b683d34f641a12e37da00e88ff3e047927a838849c3998f9f93b31c13eb70dcf6317
-MISC metadata.xml 766 BLAKE2B ff550db73357a02b91aaaec791aa89202e0f509e259ccdd8268c51b1de74121cb8ebcda8ea07974fb9d0461a10a6c79dafecc8a650a888991e0a00295af0bff3 SHA512 15a5dcefb8527784f027dbc70948897e80bf7be46ec93eef3f108fe2c0fb8dc49979e1c3ed100568613cb5024b11caa7d9133774d1aad497d2040906d2cccd98
diff --git a/sci-mathematics/drgeo/drgeo-1.1.0-r1.ebuild b/sci-mathematics/drgeo/drgeo-1.1.0-r1.ebuild
deleted file mode 100644
index c80f79a9a0cf..000000000000
--- a/sci-mathematics/drgeo/drgeo-1.1.0-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils
-
-DOC="${PN}-doc-1.5"
-
-DESCRIPTION="Interactive geometry package"
-HOMEPAGE="http://www.ofset.org/drgeo"
-SRC_URI="
-	mirror://sourceforge/ofset/${P}.tar.gz
-	mirror://sourceforge/ofset/${DOC}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="nls"
-
-RDEPEND="
-	dev-libs/libxml2:2
-	dev-scheme/guile:=[deprecated]
-	gnome-base/libglade:2.0
-	x11-libs/gtk+:2"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${P}-gcc45.patch )
-
-src_configure() {
-	default
-	# Can't make the documentation as it depends on Hyperlatex which isn't
-	# yet in portage. Fortunately HTML is already compiled for us in the
-	# tarball and so can be installed. Just create the make install target.
-	cd "${WORKDIR}"/${DOC} || die
-	econf
-}
-
-src_install() {
-	sed -i -e "s/gnome-drgenius.png/${PN}/" \
-		-e '/^Categories=/s/Application;//' \
-		${PN}.desktop || die
-	default
-	emake -C "${WORKDIR}"/${DOC}/$(usex nls "" c) DESTDIR="${D}" install
-	doicon glade/${PN}.png
-}
diff --git a/sci-mathematics/drgeo/files/drgeo-1.1.0-gcc45.patch b/sci-mathematics/drgeo/files/drgeo-1.1.0-gcc45.patch
deleted file mode 100644
index 257cbb23d111..000000000000
--- a/sci-mathematics/drgeo/files/drgeo-1.1.0-gcc45.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-Fix build with GCC 4.5, fix random SIGSEGV
-
-http://bugs.gentoo.org/show_bug.cgi?id=322211
-https://bugzilla.redhat.com/show_bug.cgi?id=454045
-
---- a/geo/drgeo_figure.h
-+++ b/geo/drgeo_figure.h
-@@ -322,4 +322,11 @@
-   gboolean showGrid;
- };
- 
-+struct
-+{
-+  drgeoPoint mouse;
-+  drgeoFigure *figure;
-+}
-+drgeoDialogData;
-+
- #endif
---- a/geo/drgeo_figure.cc
-+++ b/geo/drgeo_figure.cc
-@@ -48,13 +48,6 @@
- #include "drgeo_dialog.h"
- #include "traite.h"
- 
--extern struct
--{
--  drgeoPoint mouse;
--  drgeoFigure *figure;
--}
--drgeoDialogData;
--
- typedef struct drgeoSearchValue
- {
-   gpointer value;
-@@ -1309,7 +1302,7 @@
- gint
- drgeoFigure::preferedUndoLevel ()
- {
--  atoi (drgeoConfigGet (":undoLevel"));
-+  return atoi (drgeoConfigGet (":undoLevel"));
- }
- 
- void
---- a/geo/drgeo_dialog.cc
-+++ b/geo/drgeo_dialog.cc
-@@ -38,14 +38,6 @@
- // Used in the style dialod callback, I know it's ugly, but so easy
- static drgeoFigure *selected_figure;
- 
--struct
--{
--  drgeoPoint mouse;
--  drgeoFigure *figure;
--}
--drgeoDialogData;
--
--
- static void drgeo_edit_dialog_cb (GtkWidget * dialog,
- 				  gint button, gpointer entry);
- 
diff --git a/sci-mathematics/drgeo/metadata.xml b/sci-mathematics/drgeo/metadata.xml
deleted file mode 100644
index 433ad5443362..000000000000
--- a/sci-mathematics/drgeo/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-mathematics@gentoo.org</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Dr. Geo is a GTK2 interactive geometry software. It allows one to
-		create geometric figure plus the interactive manipulation of
-		such figure in respect with their geometric constraints. It is
-		useable in teaching situation with students from primary or
-		secondary level. It also features an integrated Scheme
-		programming language to define scripts within a figure.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">ofset</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/gmp-ecm/Manifest b/sci-mathematics/gmp-ecm/Manifest
index 96d588f0ca47..d5bb9e2ec41d 100644
--- a/sci-mathematics/gmp-ecm/Manifest
+++ b/sci-mathematics/gmp-ecm/Manifest
@@ -1,6 +1,8 @@
 DIST gmp-ecm-6.4.3.tar.gz 944719 BLAKE2B aa07f0b6c4a4b0d3bb36b596ddbaefd259b2387fa0295a829c8e239b0edde0e1f3887bff19a6b0b67083cbec7706fa41214a21eeca8b83eb4b3f7e3cc372c113 SHA512 71ccdf3b48e96b0acad45302c87a7b17a20ad289efde212a34fb11491531b96848f1824606fdab7604874ca7d8165baba4bbfbc8424e27e8844444ad0d4f56a6
 DIST gmp-ecm-6.4.4.tar.gz 941058 BLAKE2B e83f02592a8bb86285f258fefc3e302cc5168888109e7f87835b25412baf526df58e5ea38347acfd926b90fac15b4103981a14aa7b853dba0cb0168467a223e0 SHA512 039009de2d1a22de7abed2e2b843fa2bc684ddcfc45892891a24b93ad4b3640a97d2e7612ebcbdbca8db032534c226ad77c67199772b21a6139e5fa205687097
+DIST gmp-ecm-7.0.4.tar.gz 1101899 BLAKE2B 6d52364d9c752aee66510a7f6b273559bf1b7de0032fbbeff74e229ed68fd0cd1c236b480f8fc25bcad6435740e3e22b3099c8f018912918ab8f4b33dc7b8b3c SHA512 b863b9bfd26df26c3c4243686036a69110e69ca3eec5b31d4550fe713e2fac4ce70cd1d80f0614899793aa44710531aa4a21abc0fa1b99eb17f62bd92b971350
 EBUILD gmp-ecm-6.4.3-r5.ebuild 1370 BLAKE2B ad6bf30df573f77c458268b81d63157cb66ef6b0a9b6a99a2eccef27c70caac2ba51eda8d056781712fe8aa33a65128aa742ac3ac5ba5914145882a8401345ba SHA512 6c2e766207e64b1b4837720f39f99e7efc644218178a44ad994585e2febc3c13b70a2c684a89964834ccdddac6d7f60d63543b7d5f8eba90906c85f760bfb513
 EBUILD gmp-ecm-6.4.4-r1.ebuild 1474 BLAKE2B cf8ce605ccdb5a1b26db33a01989a06b8395840a84c700f7e420e8b69edc0bf4a91e03f84ce66e2d13184b10212c1e375c273d67c043adbf57e99b7462fc93eb SHA512 da6edd387bef9b397d431ee5ac7700e651a9751fb7aff1413151bf7a7f1e312def417514c7ff536a454c5b46f7405a26ad5fdbecf743f0d667313a1da6c00e22
+EBUILD gmp-ecm-7.0.4.ebuild 1163 BLAKE2B 1b47e6286c06526166e3a4e9c612ae0fee5e36e1220d9c33dbe5d93a7d2a0fa1afad87ca5f15656c9a8663044c820b09df54d6c76775da41d53926a36983ad65 SHA512 154195e3ab1ce965e8df9862a9c0571726a3426c3e3c90861913dc1937998d8be4172a2bf7207762dd2dea30a0d17d93b9257fc19a0c553306bb6f527a135493
 EBUILD gmp-ecm-9999.ebuild 1026 BLAKE2B 26e3b858f684136f9909a00f58240359cb6f09cafb64276e1c14efc7d26f13dc9b676809c8bf8d8b3b3342847b87de2b19ba5f37096a975e870694a6fb082cd3 SHA512 2f4314e9578bdc129af573c540e2f4cb26549a5a5bbfd640bdcdd50afc55b6bd05f10486a0382be4f13d4c4fac3dc93bcffd44faddfbafcafdaaf9b64d2cc579
 MISC metadata.xml 384 BLAKE2B 168807abd87bddc88522015f01126d5ec0bde8716aa38b6e619054d39e9bb12a6ffdaa3082328ecb56c0398b498c964c8e28c818d3887919fbe3065a28673f2a SHA512 a8a7aa64869c88ac293347281a80158cbd3cc84fc9f5ca56531d3d53b33601f9baa5c4f66c93508d6763dc54779a563faa09c4a473c670a9b217610efecca25c
diff --git a/sci-mathematics/gmp-ecm/gmp-ecm-7.0.4.ebuild b/sci-mathematics/gmp-ecm/gmp-ecm-7.0.4.ebuild
new file mode 100644
index 000000000000..54f7a1bbd2df
--- /dev/null
+++ b/sci-mathematics/gmp-ecm/gmp-ecm-7.0.4.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit autotools eutils flag-o-matic multilib
+
+DESCRIPTION="Elliptic Curve Method for Integer Factorization"
+HOMEPAGE="http://ecm.gforge.inria.fr/"
+SRC_URI="https://gforge.inria.fr/frs/download.php/36224/${P}.tar.gz"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blas +custom-tune -openmp static-libs test"
+
+DEPEND="
+	dev-libs/gmp:0=
+	blas? ( sci-libs/gsl )
+	openmp? ( sys-devel/gcc:*[openmp] )"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/ecm-${PV}
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+	sed -e '/libecm_la_LIBADD/s:$: -lgmp:g' -i Makefile.am || die
+	eautoreconf
+}
+
+src_configure() {
+	# --enable-shellcmd is broken
+	econf \
+		--enable-shared \
+		$(use_enable static-libs static) \
+		$(use_enable openmp) \
+		${myconf}
+}
+
+src_compile() {
+	append-ldflags "-Wl,-z,noexecstack"
+	if use custom-tune; then
+		use amd64 && cd x86_64
+		use x86 && cd pentium4
+		emake
+	fi
+	default
+}
+
+src_install() {
+	default
+	mkdir -p "${ED}/usr/include/${PN}/"
+	cp "${S}"/*.h "${ED}/usr/include/${PN}" || die "Failed to copy headers" # needed by other apps like YAFU
+}
diff --git a/sci-mathematics/num-utils/Manifest b/sci-mathematics/num-utils/Manifest
index 637db629fd67..7f8d50ba9aa4 100644
--- a/sci-mathematics/num-utils/Manifest
+++ b/sci-mathematics/num-utils/Manifest
@@ -1,6 +1,4 @@
-DIST num-utils-0.3.tar.gz 28208 BLAKE2B 7d78c69d79b3b5ea34049eea7682c25d01d9955637571ee8f7237d82b640403b1f6787c3454ac63c9a73161e053bde37f9ff14f3a799eeaf83135ed0fd505b41 SHA512 d4133062d63477ef69fa4439600e8d48b9d4944a747e3e1913a4b51e24bf07fb20cd0863c1066b90085d64ce76bc23862e2f548861aee4d8e5d36c6ac336ab7c
 DIST num-utils-0.5.tar.gz 31845 BLAKE2B fe6620dd0cc7c0d0dc03447918b525f57e9360c5d2a44a32afe7879cf8000bbce646dc271fc821531642c209bf6b356783b09e969755eb7c7af785a8a07a2462 SHA512 6f5a2a8304a0ac3cdba342ecfd28ccd926778a5fde5eed4655f973a5c921e558f0986061ec11ba6146382f63a46b1503570576370a28a0f975e361d790f03561
 DIST num-utils_0.5-11.diff.gz 11702 BLAKE2B d0f81877b3dedbd98f89d0e7448739eb6c953cc966a2a49dfc598821802837b7ade4d6ee70586febd0e72218f042dead06bc3750616960862a63c9e8134f1bef SHA512 b461771ba1c8054d83f1aea06cd6beb92945ba929ff71df9e9c02b589c59dce2f2a19e7dab76120d48de7ae2f9e30f0271ae0b873d6e220ea195e160d4347bbf
-EBUILD num-utils-0.3.ebuild 573 BLAKE2B 77c907c9e1ddcd456f0ce62f6407a7e1f8fb145963d8f0e9d13c65553e5177fe871a3c0ac3b9a76de08ed404087d1b258018a1f9d818afbe578da411a1f24dd6 SHA512 c8ab3175da4ace29c9406e044c4a59d7208c87d8dd92dca951e50c19b82b82e7fc3052e34d03c9ef1c460b7271d425684304a8e657131c49a830dbfeb51f6125
 EBUILD num-utils-0.5-r1.ebuild 1102 BLAKE2B 2fa8a6e7aa30b889a25836e1b29ff8b2ac110064c5377dddeec18038ea7869b8517959f45687a8b15c894ee0e7019a4abc2f59b72fb9e26ff56eccc0a79cc6b8 SHA512 cb32d9c43624f37bbd5331be9076d7a2d066e2d5a50ec7341fec402fedfea87477577c1813e384cb392346d060ae32be2559286e447ad104ab6d8ac5b7f6d981
 MISC metadata.xml 269 BLAKE2B 5511cf8f01948aaca0488a6ed41ed923b130bfea9ba90d49f39bff86cfbd1e956b662d07406c76ca8e7e1d2ceb54547740e9f61a0a16041e5fcf18d713f90f03 SHA512 ecf9121172cdf04793bdbf6684060c7f15fb2a25606e53d8fc7dbc78efe24e264affa600c1ee3106ce8216b7093dff66eced3f78dd6ca7bd6ee589d1c7912cd6
diff --git a/sci-mathematics/num-utils/num-utils-0.3.ebuild b/sci-mathematics/num-utils/num-utils-0.3.ebuild
deleted file mode 100644
index 17a6d211c6a1..000000000000
--- a/sci-mathematics/num-utils/num-utils-0.3.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=0
-
-DESCRIPTION="A set of programs for dealing with numbers from the command line"
-SRC_URI="http://suso.suso.org/programs/num-utils/downloads/${P}.tar.gz"
-HOMEPAGE="http://suso.suso.org/programs/num-utils/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
-	dev-lang/perl
-	!<sci-chemistry/gromacs-4"
-
-src_compile() {
-	emake || die
-}
-
-src_install () {
-	make ROOT="${D}" install || die
-	dodoc CHANGELOG GOALS MANIFEST README VERSION WARNING
-}
diff --git a/sci-mathematics/octave/Manifest b/sci-mathematics/octave/Manifest
index fb5061c15e71..a5ac00f76258 100644
--- a/sci-mathematics/octave/Manifest
+++ b/sci-mathematics/octave/Manifest
@@ -10,10 +10,13 @@ AUX octave-4.4.0-imagemagick-configure.patch 862 BLAKE2B 46e5b0ab1f7e2fd261b012b
 AUX octave-4.4.0-imagemagick.patch 850 BLAKE2B d6779333b449150299608f07d3d8a2fbce2dea1c9db7f1e04f9407ab570216e323795aeaa2964b32747f33e49d707fbea069e7dd4a438440eee4731771707125 SHA512 94d9743e2029f46e842a73ebb6315f85c5f6b0a71b797a0e43ac0f81abeccd8683d2cb84f858730c3ce40b3130012d659f571d4111f949494f6dd6bba7619477
 AUX octave-4.4.0-qt-5.11.patch 346 BLAKE2B 0e9d5a2701ca789abaf9b396e5716226ce786fe259ae84ab8cbdeeff80dcf871945e1eec5260c14525744559ee8258e96ca5e8543ab21cff27ac21723078435f SHA512 48fbd44cf0af2ecc391c18a4fdd5e0f6682998f5ab5aadf5b2f1740504b4bd40fa24c08449c4ee50d47d0307748ff7fd5a23870e6b643658583260de8b338130
 AUX octave-4.4.0-texi.patch 570 BLAKE2B 83863f20e995eb4512944d6766b09a648b0d00b434f98f25db214ef6b3bcfa504d316dad984e7330ed51d972e5caec69c42797f703595a39d6acab7128270313 SHA512 e2d0390e586e001182a31a840ed6a93b4fb6ce0dd581f64460dcf3947783dd4755a8bd277f4babb6328f04cf653f02ac681952610d7eb70165936a9d79998c3f
+AUX octave-5.1.0-pkgbuilddir.patch 1565 BLAKE2B 7b2968139e080aaa20b5372b400ac84c1754296767834011bcdda5258e7859c48ffaedcade17e8b23e2d23635a546c6a726061e8b4679913ff5b204a26cd0ef4 SHA512 28dcebc3a904cf048cb0568591c6c55616d40f6ca80982a232489a51ec92505dca186043ee3750d8a3f3782149ef1861332a8486466fba2898f0084adf0acb90
 DIST octave-4.2.2.tar.gz 25624087 BLAKE2B c46de90d9a985c2b6b4f87b94b56f2ba4fb648ca0a0aff1f64e9b9d27a6d791e8657c2bff0c4daa3de5ac3622c23b34724e740ec1fe0f1a71d8f416c9f58d88a SHA512 b94edd79adc0e19229bb654037910201b51b6cfa373d63de5e3aa69e9b659b2e2790e2d2b4b5e8d2f12b26846c20ba5c12eae657155c8329e85e970f738d08c2
 DIST octave-4.4.0.tar.gz 29009355 BLAKE2B 3f7b4a6e1262cd0009f8649a570749acc2dc8b42aa1f88a6ce69b9c6bb99a95390f5a153c391a60ac118dc1e87f15596c7225764634c6076bb1ab3dfa4e09bcc SHA512 6a167a4a6a2f6ae70511f13b14feea0ce3efcc964227c93f3195adb3a1f1f28dda56f86a2e1c7c5e9f54891d2846fb96972092387e3da41f2e04cb700606ffc2
 DIST octave-4.4.1.tar.gz 28626462 BLAKE2B 0ea7a9b5840c7afdf20dff36e896b37c1c69eb8799ba48722c02f9636591b849f26f56720a75293c11c1000d0088e07373aa84ef7d360436eb095fc0a2e721a6 SHA512 21a1f13e2145fa530f2169254d19442b572745d65b91453ba1f552f6eda6aecfead57dbe0260b3293a29db0aa0f27cfd4f26df332e6d640848a822b20c1232f8
+DIST octave-5.1.0.tar.gz 32034788 BLAKE2B d387f41f6ae826b35735fc4208d71be84076a81544f5cd0e3d5410f41a70eebb5b0b3bbf19e4344b88901869d54f2759259dc374c44a430f681d3b0c32cb02cb SHA512 a842fb50c13f25e9d425fe9a2c71d9433d7e125747d2175efe0c9b2a780c799d9ce1ee085b5a13fbfedb7990b0ba5d11079d880ddb3bdb66782efc321390eebb
 EBUILD octave-4.2.2.ebuild 5112 BLAKE2B 2f08b20c4557a30b1b8bb3608c400805cf21af1f438ffc8e5f8cc54576b5c6116bfc009bb29c33b9a4f69e29e0f423994fda8cc4b04967209179d4a90a7d7d7d SHA512 4a033bec4259b063ed3c5008881c6ff57e061e7e769b9481f3dd14af3e004711d0a9f221b0afc9fce83386d102062d84d0813fd01cee3b240f4266b0c0371039
 EBUILD octave-4.4.0.ebuild 5092 BLAKE2B c78da0de6de2550d58131a36336d49d021ef203c42f3f1889913c01d1b0ee24af2c446bb30d6f56043c368d7ec3943d50637a939e65638bbd6ddba6030054614 SHA512 fc3e27c85ed9a5e54ce3acad53bd8d6122dace79b62cb02a155a4abe93c75209f883556761ed20ef78e6a64d8dc97c6c876b9f3a918898119db46cbef21d66dc
 EBUILD octave-4.4.1.ebuild 5190 BLAKE2B 6aeaf6fb0c50188027786ed55fd63f223a6d403ded9fa5736b0883aa0c3d443cc3147bd1fcfef6ea011e1f023057ba3fe90c29cb3e406d1f293f3a72698eefbe SHA512 726b0787936c803a03ff1669c1cdf5d29f926c13fe1c2010802829098a62502c0245ad69cad476b8d4149e7f97f2ca5c680fd553cc6708159654a61ad0434ed7
+EBUILD octave-5.1.0.ebuild 5086 BLAKE2B 96cedb79e27e8f1c846b467b28c2d62f999a9c3c16f3d9c3a9a08cd5b683ddcf8cac993cc38f4d0602b2a53d989fc0c383143eb19375d13386e3efcef4870702 SHA512 89f98419f393b8d0df576f275ec97adce10f75d815ded2ff7a89956ff5bedadac110be9c086e78d790a7d3d65a86f8c8188d223e1889a5a2d5689fc1001b82bd
 MISC metadata.xml 1199 BLAKE2B f1daa0330bdc0362c68458ce6e7145118dd8a9d1a3bcbcc76c04ccdffe700c9d6f71b5e8b7f05b5ed0154352a213ce7b5177284919362585fedb0dbd8b68cbca SHA512 aebb1728f0ca59ba83b649eea72c267c530efc0b97b12f0d7958ba8de0f482fcb37245cf93bc188c9368686e0feafc44da4a7dd97d6bab8246309945fee8f7a4
diff --git a/sci-mathematics/octave/files/octave-5.1.0-pkgbuilddir.patch b/sci-mathematics/octave/files/octave-5.1.0-pkgbuilddir.patch
new file mode 100644
index 000000000000..56a133b7f359
--- /dev/null
+++ b/sci-mathematics/octave/files/octave-5.1.0-pkgbuilddir.patch
@@ -0,0 +1,43 @@
+Index: octave-5.1.0/scripts/pkg/private/install.m
+===================================================================
+--- octave-5.1.0.orig/scripts/pkg/private/install.m
++++ octave-5.1.0/scripts/pkg/private/install.m
+@@ -62,7 +62,14 @@ function install (files, handle_deps, pr
+     for i = 1:length (files)
+       tgz = files{i};
+ 
+-      if (exist (tgz, "file"))
++      ## The filename pointed to an uncompressed package to begin with.
++      if (exist (tgz, "dir"))
++        if (tgz(1) == '/')
++          packdir = tgz;
++        else
++          packdir = fullfile (pwd(), tgz);
++        endif
++      elseif (exist (tgz, "file"))
+         ## Create a temporary directory.
+         tmpdir = tempname ();
+         tmpdirs{end+1} = tmpdir;
+@@ -89,20 +96,12 @@ function install (files, handle_deps, pr
+         if (length (dirlist) > 3)
+           error ("bundles of packages are not allowed");
+         endif
+-      endif
+ 
+-      ## The filename pointed to an uncompressed package to begin with.
+-      if (isfolder (tgz))
+-        dirlist = {".", "..", tgz};
++        ## The two first entries of dirlist are "." and "..".
++        packdir = fullfile (tmpdir, dirlist{3});
+       endif
+ 
+       if (exist (tgz, "file") || isfolder (tgz))
+-        ## The two first entries of dirlist are "." and "..".
+-        if (exist (tgz, "file"))
+-          packdir = fullfile (tmpdir, dirlist{3});
+-        else
+-          packdir = fullfile (pwd (), dirlist{3});
+-        endif
+         packdirs{end+1} = packdir;
+ 
+         ## Make sure the package contains necessary files.
diff --git a/sci-mathematics/octave/octave-5.1.0.ebuild b/sci-mathematics/octave/octave-5.1.0.ebuild
new file mode 100644
index 000000000000..f347d4a6cfb1
--- /dev/null
+++ b/sci-mathematics/octave/octave-5.1.0.ebuild
@@ -0,0 +1,192 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools flag-o-matic fortran-2 gnome2-utils java-pkg-opt-2 pax-utils toolchain-funcs xdg-utils
+
+DESCRIPTION="High-level interactive language for numerical computations"
+LICENSE="GPL-3"
+HOMEPAGE="https://www.gnu.org/software/octave/"
+SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
+
+SLOT="0/${PV}"
+IUSE="curl doc fftw +glpk gnuplot graphicsmagick gui hdf5 +imagemagick java libressl opengl
+	portaudio postscript +qhull +qrupdate readline sndfile +sparse ssl static-libs X zlib"
+KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	app-arch/bzip2
+	app-text/ghostscript-gpl
+	dev-libs/libpcre:3=
+	sys-libs/ncurses:0=
+	sys-libs/zlib
+	virtual/blas
+	virtual/lapack
+	curl? ( net-misc/curl:0= )
+	fftw? ( sci-libs/fftw:3.0= )
+	glpk? ( sci-mathematics/glpk:0= )
+	gnuplot? ( sci-visualization/gnuplot )
+	gui? (
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+		dev-qt/qthelp:5
+		dev-qt/qtnetwork:5
+		dev-qt/qtopengl:5
+		dev-qt/qtprintsupport:5
+		dev-qt/qtwidgets:5
+		x11-libs/qscintilla:=
+	)
+	hdf5? ( sci-libs/hdf5:0= )
+	imagemagick? (
+		!graphicsmagick? ( >=media-gfx/imagemagick-7:=[cxx] )
+		graphicsmagick? ( media-gfx/graphicsmagick:=[cxx] )
+	)
+	java? ( >=virtual/jre-1.6.0:* )
+	opengl? (
+		media-libs/freetype:2=
+		media-libs/fontconfig:1.0=
+		virtual/glu
+		>=x11-libs/fltk-1.3:1=[opengl,xft]
+		x11-libs/gl2ps:0=
+	)
+	ssl? (
+		 !libressl? ( dev-libs/openssl:0= )
+		 libressl? ( dev-libs/libressl:0= )
+	)
+	portaudio? ( media-libs/portaudio )
+	postscript? (
+		app-text/epstool
+		media-gfx/pstoedit
+		media-gfx/transfig
+	)
+	qhull? ( media-libs/qhull:0= )
+	qrupdate? ( sci-libs/qrupdate:0= )
+	readline? ( sys-libs/readline:0= )
+	sndfile? ( media-libs/libsndfile )
+	sparse? (
+		sci-libs/arpack:0=
+		sci-libs/camd:0=
+		sci-libs/ccolamd:0=
+		sci-libs/cholmod:0=
+		sci-libs/colamd:0=
+		sci-libs/cxsparse:0=
+		sci-libs/umfpack:0=
+	)
+	X? ( x11-libs/libX11:0= )"
+DEPEND="${RDEPEND}
+	dev-util/gperf
+	sys-apps/texinfo
+	virtual/pkgconfig
+	doc? (
+		dev-texlive/texlive-fontsrecommended
+		dev-texlive/texlive-plaingeneric
+		dev-texlive/texlive-metapost
+		virtual/latex-base
+	)
+	gui? ( dev-qt/linguist-tools:5 )
+	java? ( >=virtual/jdk-1.6.0 )
+	qrupdate? ( app-misc/pax-utils )
+	sparse? ( app-misc/pax-utils )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.4.0-texi.patch
+	"${FILESDIR}"/${PN}-4.2.0-disable-getcwd-path-max-test-as-it-is-too-slow.patch
+	"${FILESDIR}"/${PN}-4.4.0-imagemagick-configure.patch
+	"${FILESDIR}"/${PN}-4.4.0-imagemagick.patch
+	"${FILESDIR}"/${PN}-5.1.0-pkgbuilddir.patch
+	"${FILESDIR}"/${PN}-4.2.2-ncurses-pkgconfig.patch
+	"${FILESDIR}"/${PN}-4.2.0-zlib-underlinking.patch
+	"${FILESDIR}"/${PN}-4.4.0-qt-5.11.patch
+)
+
+src_prepare() {
+	# nasty prefix hacks for fltk:1 linking
+	if use prefix; then
+		use opengl && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/fltk-1"
+	fi
+
+	# occasional fail on install, force regeneration (bug #401189)
+	rm doc/interpreter/contributors.texi || die
+
+	default
+	eautoreconf
+}
+
+src_configure() {
+	# unfortunate dependency on mpi from hdf5 (bug #302621)
+	use hdf5 && has_version sci-libs/hdf5[mpi] && \
+		export CXX=mpicxx CC=mpicc FC=mpif77 F77=mpif77
+
+	econf \
+		--localstatedir="${EPREFIX}/var/state/octave" \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \
+		--disable-64 \
+		--disable-jit \
+		--enable-shared \
+		--with-z \
+		--with-bz2 \
+		$(use_enable static-libs static) \
+		$(use_enable doc docs) \
+		$(use_enable java) \
+		$(use_enable readline) \
+		$(use_with curl) \
+		$(use_with fftw fftw3) \
+		$(use_with fftw fftw3f) \
+		$(use_enable fftw fftw-threads) \
+		$(use_with glpk) \
+		$(use_with hdf5) \
+		$(use_with imagemagick magick $(usex graphicsmagick GraphicsMagick ImageMagick)) \
+		$(use_with opengl) \
+		$(use_with opengl fltk) \
+		$(use_with ssl openssl) \
+		$(use_with portaudio) \
+		$(use_with qhull) \
+		$(use_with qrupdate) \
+		$(use_with gui qt 5) \
+		$(use_with sndfile) \
+		$(use_with sparse arpack) \
+		$(use_with sparse umfpack) \
+		$(use_with sparse colamd) \
+		$(use_with sparse ccolamd) \
+		$(use_with sparse cholmod) \
+		$(use_with sparse cxsparse) \
+		$(use_with X x)
+}
+
+src_compile() {
+	export VARTEXFONTS="${T}/fonts" # otherwise it will write to /var/cache/fonts/ and trip sandbox
+	default
+	if use java; then
+		pax-mark m "${S}/src/.libs/octave-cli"
+	fi
+}
+
+src_install() {
+	default
+	if use doc; then
+		dodoc $(find doc -name '*.pdf')
+	else
+		# bug 566134, macros.texi is installed by make install if use doc
+		insinto /usr/share/${PN}/${PV}/etc
+		doins doc/interpreter/macros.texi
+	fi
+	[[ -e test/fntests.log ]] && dodoc test/fntests.log
+	use java && \
+		java-pkg_regjar "${ED%/}/usr/share/${PN}/${PV}/m/java/octave.jar"
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}/${PV}" > 99octave || die
+	doenvd 99octave
+}
+
+pkg_postinst() {
+	gnome2_icon_cache_update
+	xdg_mimeinfo_database_update
+	xdg_desktop_database_update
+}
+
+pkg_postrm() {
+	gnome2_icon_cache_update
+	xdg_mimeinfo_database_update
+	xdg_desktop_database_update
+}
diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 1dd38bb58c05..c58fb3ea5fa1 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -7,26 +7,42 @@ AUX rstudio-1.0.44-systemd.patch 1147 BLAKE2B ca1b24c2544ff2cb6b9e7a91b4ce25eda7
 AUX rstudio-1.1.357-clang-pandoc.patch 3240 BLAKE2B bc7f55d2f2cea64643d02af314afbbd0df1d986889d0d3a2bbf6878e9f8ec7d73710c7e631bf0cbf04b4ecf4142236ef7a1dc0a073d34958a8bd0828594f605d SHA512 3a2fc154f934b4bbd92df6359dc26c27bf2f4f06b2dde572faba3c083879c8e0e98ed776701282d9f3a5cb3f4ac2416e04e6a30beedf4ffa5cbeca3a7e72421b
 AUX rstudio-1.1.453-boost-1.67.0.patch 1920 BLAKE2B d360259929a73ca6ed7b59997e34dfb2f40992ad6a25372fa2465d07c6df93838d62f5c9dd54b3b45850056bdcba24d20f84eda9480103e71feeac0b20df0a1b SHA512 250c16695c42b03d59ed690de8fc38494ac52047f5fe88b82df431082d524a396266c2b7e8c6afbf3b25e08102d99ef37b3892d62e7bc134f872718880660709
 AUX rstudio-1.1.453-core.patch 5843 BLAKE2B 9634a1d619c7e32e672d64ce90c092a9451499ffb27104a5228b4665abeffe7618f92ac04c29b6a3278c2702fe1361be43ba9eb1616acef71c42d39c68df9e65 SHA512 64e50dc812fb60ce6d8b17c6ea0eb6cfa055faa3a235d12e84ecb2691fcc90ef457d4eddc6e8029145fc3e919336fb0c91c293767c2d2f27bd542508c1e458aa
-AUX rstudio-1.1.463-boost-1.69.0_p1.patch 27177 BLAKE2B 7d902104856cff7f6f3c2eef5f5712bd86112d5f4f7149d05bced5084d4e57f27b8c67975fc6ce6f40980e8b1544c528db440142d82d81775fe773189096d4cc SHA512 3b6d53afd9233400edce3dc7cfd18cd1b1804707c22a6efbf821527d19517d1c643272e947e5550be8735bd00829cf9be800dca84bc60f91e9dded747deebae3
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+AUX rstudio-1.1.463-boost-1.69.0_p1.patch 18663 BLAKE2B b6431c931c97bdad30756e62510ad839c86f77e2474faace7202ef596fe6d2e06659fdd82d78135456a7ed9b343df0a309432438dcd7a87b5cde2e0b690e3be3 SHA512 2c86971f29059c22d97680cd8ccbcdab19873f28929b71079f1d3cc004ea3625ebc4644f49c0ac9fbe4726b8d60c76cbbd882e8712e76cd0c939a2a31fe6f945
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+AUX rstudio-1.2.1335-fix-ptr-int-compare.patch 595 BLAKE2B 8db7be4c0be67670d60a8f096faa58b13a6dc87194d0997cf97768d8fd67e2c74b84c4de2a8f4502bbd9cf262293b8fe18f4d05428394dcc70ebc8962a969923 SHA512 2f083f036f3594af206fd71db5b761ae6a536e99e4b51264234a7d8169db252b0494da19d5e9d319817a84f6002f64ccb388bc6e0a42bf439c1365618da5626f
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 EBUILD rstudio-1.1.453.ebuild 8502 BLAKE2B 9cf5aee42e422d77798a65b5447ef2027b4ca7a2cc2c35d37c7ec44109956ab1efaf253c4fe54c1c401ad10e50947898e8fd632894df2ad99ebb0c60046cf9ac SHA512 087dd2e5fdac0bb6bd261d40a8ef53f50de7aa1e922eb2a20eab2a3560431748e202ba9de1ae7adf1fd65847b14627628ce945894c94903f8ebfc3287641118b
-EBUILD rstudio-1.1.463.ebuild 8662 BLAKE2B 80861e38451ce653420d601c05ed2df9db0d5ceeb95758c8290abac212f9161e1ce3d09b6fba8b04a3a88b7028ff67f52577f6c626bf6a485c79876a02735e01 SHA512 bbfe44bf555d35a8eb6887760daead2a57e5d01d30eea39741a9f6202d27b9fff6b61af2bfe092be3841aedcd1bb92cdd82811715418b612756d738a8f7cb192
+EBUILD rstudio-1.1.463-r1.ebuild 8691 BLAKE2B e9cc9c2652c2f0193bfe5093c3a14a51f6d499a6e1c65b549ce8619017aaa8e196a55d8af3683b70ed3a139982e2e67ff4b829af0f8b554e8fb895aaab02d5df SHA512 9c98ecb0213f499c415e565d4da05d17c68c0276bc93fb5e9bee8a23057064bbcd32bac54c8a5bf5a111586438670d52d5bf92cde2947adc9e5911f72d6915b1
+EBUILD rstudio-1.1.463.ebuild 8714 BLAKE2B 415be08177b519e1e0863c60d3b3cceb241615862afb1d03f60367e03da3516ee32c45acef68e34951721290e7e775afec2c690534ccad3742b154709053c2eb SHA512 155cc3f01dd2e8ea20b5e061b5aa946cf69a42ed536db5e89352c759fdc4b2e1c7733d6181c3560beca2fa7e5571bc65ccafd0e9e33545229f1053cd20d13756
+EBUILD rstudio-1.2.1335.ebuild 8630 BLAKE2B 3a403fe159129f869b06dd59ede3b279ef9b20fdd467bfdc14b57acabf6191a2d1f4e4a2575f4728543440cbd00957709122faccae4e1ff89393ae96442ccfcf SHA512 a98ff2097ec07fef51c838d1c5705cdf34ac8ac40699c692f1038c926548e7906dacd5a475baf365be941186c1ebe8d929d198986b5e4dfe2404db262c2b9f25
 MISC metadata.xml 590 BLAKE2B 53dc62775e118c9c26ee05e20ee1da1ac31b6a6b74cf7dac410856fe4e0cce40fbb800c7a03e60f59e14442baf3aad866ad42616ad5fbb5724f7f6d8c1636eea SHA512 7111442aaa52da1e554c34f824113ec0e227798dd11b0ea9148b81e7a31c08b2a527b9995e3adb9363c7a4f2a8594f30cbd4a179545bf31d69f07d5558c20f52
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
index aa3db25f3c01..a7a48572de30 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
@@ -1,4 +1,4 @@
---- /dev/null	2018-11-10 15:32:26.332997437 +1100
+--- /dev/null	2019-03-19 11:03:33.121000004 +1100
 +++ rstudio-1.1.463/src/cpp/core/include/core/BoostSignals.hpp	2018-11-17 21:24:35.285976284 +1100
 @@ -0,0 +1,40 @@
 +/*
@@ -458,223 +458,3 @@
  };
  
  ProjectContext& projectContext();
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
-@@ -16,7 +16,7 @@
- #ifndef SESSION_PLOTS_HPP
- #define SESSION_PLOTS_HPP
- 
--#include <boost/signals.hpp>
-+#include <core/BoostSignals.hpp>
- 
- namespace rstudio {
- namespace core {
-@@ -35,9 +35,9 @@
- 
- struct Events : boost::noncopyable
- {
--   boost::signal<void()> onBeforeNewPlot;
--   boost::signal<void()> onBeforeNewGridPage;
--   boost::signal<void()> onNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
-+   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
- };
- 
- Events& events();
---- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
-@@ -15,11 +15,11 @@
- 
- #include "SessionSourceCpp.hpp"
- 
--#include <boost/signal.hpp>
- #include <boost/algorithm/string/trim.hpp>
- #include <boost/algorithm/string/predicate.hpp>
- #include <boost/algorithm/string/join.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
- #include <core/StringUtils.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -142,7 +142,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -219,7 +219,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -363,7 +363,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -16,6 +16,8 @@
- #include "SessionRmdNotebook.hpp"
- #include "NotebookCapture.hpp"
- 
-+#include <boost/make_shared.hpp>
-+
- namespace rstudio {
- namespace session {
- namespace modules {
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -441,7 +441,7 @@
-    }
- 
-    // unhook all our event handlers
--   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
-+   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
-    {
-       connection.disconnect();
-    }
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
-@@ -18,8 +18,7 @@
- 
- #include <session/SessionModuleContext.hpp>
- 
--#include <boost/signal.hpp>
--
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #include <r/RSexp.hpp>
-@@ -99,7 +98,7 @@
-    bool hasErrors_;
- 
-    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
--   std::vector<boost::signals::connection> connections_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
- };
- 
- } // namespace notebook
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -20,11 +20,12 @@
- 
- #include <boost/format.hpp>
- #include <boost/foreach.hpp>
--#include <boost/signals/connection.hpp>
- 
--#include <core/system/FileMonitor.hpp>
--#include <core/StringUtils.hpp>
-+#include <core/BoostSignals.hpp>
- #include <core/Exec.hpp>
-+#include <core/StringUtils.hpp>
-+
-+#include <core/system/FileMonitor.hpp>
- 
- #include <session/SessionModuleContext.hpp>
- 
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,8 +18,10 @@
- #define SESSION_NOTEBOOK_PLOTS_HPP
- 
- #include <boost/function.hpp>
--#include <boost/signals/connection.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/FilePath.hpp>
-+
- #include <r/RSexp.hpp>
- 
- #include "NotebookCapture.hpp"
-@@ -80,9 +82,9 @@
- 
-    unsigned lastOrdinal_;
- 
--   boost::signals::connection onBeforeNewPlot_;
--   boost::signals::connection onBeforeNewGridPage_;
--   boost::signals::connection onNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
-+   RSTUDIO_BOOST_CONNECTION onNewPlot_;
- 
-    double width_;
-    double height_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
-@@ -87,7 +87,7 @@
-       pInput_->enque(kThreadQuitCommand);
- 
-       // unregister handlers
--      BOOST_FOREACH(boost::signals::connection connection, handlers_)
-+      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
-       {
-          connection.disconnect();
-       }
-@@ -651,7 +651,7 @@
-    boost::shared_ptr<ChunkExecContext> execContext_;
- 
-    // registered signal handlers
--   std::vector<boost::signals::connection> handlers_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
- 
-    // the thread which submits console input, and the queue which feeds it
-    boost::thread console_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,7 +18,8 @@
- #define SESSION_RMARKDOWN_NOTEBOOK_HPP
- 
- #include <ctime>
--#include <boost/signals.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #define kChunkLibDir "lib"
-@@ -76,24 +77,24 @@
- struct Events : boost::noncopyable
- {
-    // Document {0}, chunk {1} from context id {3} execution completed
--   boost::signal<void(const std::string&, const std::string&,
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
-                       const std::string&)> 
-                 onChunkExecCompleted;
- 
-    // Document {0}, chunk {1} had console output of type {2} and text {3}
--   boost::signal<void(const std::string&, const std::string&, int, 
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
-                 const std::string&)>
-                 onChunkConsoleOutput;
- 
--   boost::signal<void(const core::FilePath&, const core::FilePath&, 
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
-                       const core::json::Value& metadata, unsigned ordinal)> 
-                          onPlotOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onHtmlOutput;
--   boost::signal<void(const core::json::Object&)> onErrorOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onDataOutput;
--   boost::signal<void(Condition condition, const std::string& message)> 
-+   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
-                          onCondition;
- };
- 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
index 961723fd224f..d90ce005a1a0 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
@@ -1,167 +1,220 @@
---- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
-+++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:41:02.712507842 +1100
-@@ -175,6 +175,9 @@
-       set(Boost_USE_STATIC_LIBS ON)
-       set(BOOST_INCLUDEDIR  ${RSTUDIO_TOOLS_BOOST}/include)
-       find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
- 
-       # define library list manually (find_package doesn't always pick them up)
-       set(BOOST_LIB_DIR ${RSTUDIO_TOOLS_BOOST}/lib)
-@@ -184,11 +187,15 @@
-       message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
-    else()
-       add_definitions(-DRSTUDIO_BOOST_NAMESPACE=boost)
-+      find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
-       find_package(Boost ${BOOST_VERSION} REQUIRED COMPONENTS ${BOOST_LIBS})
-       message(STATUS "Using system Boost ${BOOST_VERSION}")
-    endif()
- 
--   # WIN32 BOOST
-+# WIN32 BOOST
- else()
-    # hard-code to our own prebuilt boost libs
-    add_definitions(-DRSTUDIO_BOOST_NAMESPACE=rstudio_boost)
-@@ -211,14 +218,14 @@
- # allow opt-in to using Boost.Signals2
- # TODO: remove this in RStudio v1.3 and port to signals2
- if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
--   if (BOOST_VERSION VERSION_LESS 1.69.0)
-+   if (Boost_VERSION VERSION_LESS 1.69.0)
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
-    else()
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
-    endif()
- endif()
- 
--message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
-+message(STATUS "Using Boost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
- add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
- 
- # add boost as system include directory
---- rstudio-1.1.463-orig/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-11-17 21:41:02.713507852 +1100
-@@ -75,9 +75,9 @@
-    const std::string& name() const { return name_; }
-    const boost::optional<std::string>& defaultValue() const { return defaultValue_; }
-    boost::tribool hasDefault() const { return hasDefault_; }
--   bool isUsed() const { return isUsed_; }
-+   bool isUsed() const { return bool(isUsed_); }
-    void setIsUsed(bool value) { isUsed_ = value; }
--   bool isMissingnessHandled() const { return isMissingnessHandled_; }
-+   bool isMissingnessHandled() const { return bool(isMissingnessHandled_); }
-    void setMissingnessHandled(bool value) { isMissingnessHandled_ = value; }
+--- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
+@@ -16,7 +16,7 @@
+ #ifndef SESSION_PLOTS_HPP
+ #define SESSION_PLOTS_HPP
+ 
+-#include <boost/signals.hpp>
++#include <core/BoostSignals.hpp>
+ 
+ namespace rstudio {
+ namespace core {
+@@ -35,9 +35,9 @@
+ 
+ struct Events : boost::noncopyable
+ {
+-   boost::signal<void()> onBeforeNewPlot;
+-   boost::signal<void()> onBeforeNewGridPage;
+-   boost::signal<void()> onNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
++   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
+ };
+ 
+ Events& events();
+--- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
+@@ -15,11 +15,11 @@
+ 
+ #include "SessionSourceCpp.hpp"
+ 
+-#include <boost/signal.hpp>
+ #include <boost/algorithm/string/trim.hpp>
+ #include <boost/algorithm/string/predicate.hpp>
+ #include <boost/algorithm/string/join.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/StringUtils.hpp>
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -142,7 +142,7 @@
+       LOG_ERROR(error);
     
- private:
-@@ -130,7 +130,7 @@
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -219,7 +219,7 @@
+       LOG_ERROR(error);
     
-    bool isPrimitive()
-    {
--      return isPrimitive_ == true;
-+      return bool(isPrimitive_);
-    }
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -363,7 +363,7 @@
+       LOG_ERROR(error);
     
-    void setIsPrimitive(bool isPrimitive)
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionRParser.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionRParser.cpp	2018-11-17 21:41:02.714507862 +1100
-@@ -390,7 +390,7 @@
-    if (!failed)
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -16,6 +16,8 @@
+ #include "SessionRmdNotebook.hpp"
+ #include "NotebookCapture.hpp"
+ 
++#include <boost/make_shared.hpp>
++
+ namespace rstudio {
+ namespace session {
+ namespace modules {
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -441,7 +441,7 @@
+    }
+ 
+    // unhook all our event handlers
+-   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
++   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
     {
-       DEBUG("--- Found function in pkgInfo index: " << *fnInfo.binding());
--      return fnInfo.performsNse();
-+      return bool(fnInfo.performsNse());
+       connection.disconnect();
     }
-    
-    // Handle some special cases first.
---- rstudio-1.1.463-orig/src/tools/clang-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/clang-ubsan-build	2018-11-17 21:41:02.714507862 +1100
-@@ -10,19 +10,19 @@
- 
- : ${RSTUDIO_USE_LIBCXX="Yes"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.56.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.56.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/gcc-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/gcc-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -19,19 +19,19 @@
- # NOTE: Boost 1.50.0 not compatible with gcc-6
- : ${RSTUDIO_USE_LIBCXX="No"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.54.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.54.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/xcode-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/xcode-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -15,13 +15,13 @@
- # sanitizers released with newer versions of clang)
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp -GXcode                 \
--    -DLIBR_HOME="${R_HOME}"          \
--    -DLIBR_INCLUDE_DIRS="${R_INCL}"  \
--    -DLIBR_DOC_DIR="${R_DOCS}"       \
--    -DRSTUDIO_USE_LIBCXX="Yes"       \
--    -DRSTUDIO_USE_SYSTEM_BOOST="Yes" \
--    -DRSTUDIO_BOOST_VERSION="1.56.0" \
-+cmake ../cpp -GXcode                           \
-+    -DLIBR_HOME="${R_HOME}"                    \
-+    -DLIBR_INCLUDE_DIRS="${R_INCL}"            \
-+    -DLIBR_DOC_DIR="${R_DOCS}"                 \
-+    -DRSTUDIO_USE_LIBCXX="Yes"                 \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="Yes"           \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="1.56.0" \
-     "$@"
- cmake ../cpp -DLIBR_LIBRARIES="${R_LIBS}/libR.dylib"
- cd ..
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
+@@ -18,8 +18,7 @@
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+-#include <boost/signal.hpp>
+-
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #include <r/RSexp.hpp>
+@@ -99,7 +98,7 @@
+    bool hasErrors_;
+ 
+    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
+-   std::vector<boost::signals::connection> connections_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
+ };
+ 
+ } // namespace notebook
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -20,11 +20,12 @@
+ 
+ #include <boost/format.hpp>
+ #include <boost/foreach.hpp>
+-#include <boost/signals/connection.hpp>
+ 
+-#include <core/system/FileMonitor.hpp>
+-#include <core/StringUtils.hpp>
++#include <core/BoostSignals.hpp>
+ #include <core/Exec.hpp>
++#include <core/StringUtils.hpp>
++
++#include <core/system/FileMonitor.hpp>
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,8 +18,10 @@
+ #define SESSION_NOTEBOOK_PLOTS_HPP
+ 
+ #include <boost/function.hpp>
+-#include <boost/signals/connection.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/FilePath.hpp>
++
+ #include <r/RSexp.hpp>
+ 
+ #include "NotebookCapture.hpp"
+@@ -80,9 +82,9 @@
+ 
+    unsigned lastOrdinal_;
+ 
+-   boost::signals::connection onBeforeNewPlot_;
+-   boost::signals::connection onBeforeNewGridPage_;
+-   boost::signals::connection onNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
++   RSTUDIO_BOOST_CONNECTION onNewPlot_;
+ 
+    double width_;
+    double height_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
+@@ -87,7 +87,7 @@
+       pInput_->enque(kThreadQuitCommand);
+ 
+       // unregister handlers
+-      BOOST_FOREACH(boost::signals::connection connection, handlers_)
++      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
+       {
+          connection.disconnect();
+       }
+@@ -651,7 +651,7 @@
+    boost::shared_ptr<ChunkExecContext> execContext_;
+ 
+    // registered signal handlers
+-   std::vector<boost::signals::connection> handlers_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
+ 
+    // the thread which submits console input, and the queue which feeds it
+    boost::thread console_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,7 +18,8 @@
+ #define SESSION_RMARKDOWN_NOTEBOOK_HPP
+ 
+ #include <ctime>
+-#include <boost/signals.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #define kChunkLibDir "lib"
+@@ -76,24 +77,24 @@
+ struct Events : boost::noncopyable
+ {
+    // Document {0}, chunk {1} from context id {3} execution completed
+-   boost::signal<void(const std::string&, const std::string&,
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
+                       const std::string&)> 
+                 onChunkExecCompleted;
+ 
+    // Document {0}, chunk {1} had console output of type {2} and text {3}
+-   boost::signal<void(const std::string&, const std::string&, int, 
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
+                 const std::string&)>
+                 onChunkConsoleOutput;
+ 
+-   boost::signal<void(const core::FilePath&, const core::FilePath&, 
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
+                       const core::json::Value& metadata, unsigned ordinal)> 
+                          onPlotOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onHtmlOutput;
+-   boost::signal<void(const core::json::Object&)> onErrorOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onDataOutput;
+-   boost::signal<void(Condition condition, const std::string& message)> 
++   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
+                          onCondition;
+ };
+ 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
new file mode 100644
index 000000000000..961723fd224f
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
@@ -0,0 +1,167 @@
+--- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
++++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:41:02.712507842 +1100
+@@ -175,6 +175,9 @@
+       set(Boost_USE_STATIC_LIBS ON)
+       set(BOOST_INCLUDEDIR  ${RSTUDIO_TOOLS_BOOST}/include)
+       find_package(Boost ${BOOST_VERSION} REQUIRED)
++      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
++         list(REMOVE_ITEM BOOST_LIBS signals)
++      endif()
+ 
+       # define library list manually (find_package doesn't always pick them up)
+       set(BOOST_LIB_DIR ${RSTUDIO_TOOLS_BOOST}/lib)
+@@ -184,11 +187,15 @@
+       message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
+    else()
+       add_definitions(-DRSTUDIO_BOOST_NAMESPACE=boost)
++      find_package(Boost ${BOOST_VERSION} REQUIRED)
++      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
++         list(REMOVE_ITEM BOOST_LIBS signals)
++      endif()
+       find_package(Boost ${BOOST_VERSION} REQUIRED COMPONENTS ${BOOST_LIBS})
+       message(STATUS "Using system Boost ${BOOST_VERSION}")
+    endif()
+ 
+-   # WIN32 BOOST
++# WIN32 BOOST
+ else()
+    # hard-code to our own prebuilt boost libs
+    add_definitions(-DRSTUDIO_BOOST_NAMESPACE=rstudio_boost)
+@@ -211,14 +218,14 @@
+ # allow opt-in to using Boost.Signals2
+ # TODO: remove this in RStudio v1.3 and port to signals2
+ if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
+-   if (BOOST_VERSION VERSION_LESS 1.69.0)
++   if (Boost_VERSION VERSION_LESS 1.69.0)
+       set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
+    else()
+       set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
+    endif()
+ endif()
+ 
+-message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
++message(STATUS "Using Boost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
+ add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
+ 
+ # add boost as system include directory
+--- rstudio-1.1.463-orig/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-11-17 21:41:02.713507852 +1100
+@@ -75,9 +75,9 @@
+    const std::string& name() const { return name_; }
+    const boost::optional<std::string>& defaultValue() const { return defaultValue_; }
+    boost::tribool hasDefault() const { return hasDefault_; }
+-   bool isUsed() const { return isUsed_; }
++   bool isUsed() const { return bool(isUsed_); }
+    void setIsUsed(bool value) { isUsed_ = value; }
+-   bool isMissingnessHandled() const { return isMissingnessHandled_; }
++   bool isMissingnessHandled() const { return bool(isMissingnessHandled_); }
+    void setMissingnessHandled(bool value) { isMissingnessHandled_ = value; }
+    
+ private:
+@@ -130,7 +130,7 @@
+    
+    bool isPrimitive()
+    {
+-      return isPrimitive_ == true;
++      return bool(isPrimitive_);
+    }
+    
+    void setIsPrimitive(bool isPrimitive)
+--- rstudio-1.1.463-orig/src/cpp/session/modules/SessionRParser.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/SessionRParser.cpp	2018-11-17 21:41:02.714507862 +1100
+@@ -390,7 +390,7 @@
+    if (!failed)
+    {
+       DEBUG("--- Found function in pkgInfo index: " << *fnInfo.binding());
+-      return fnInfo.performsNse();
++      return bool(fnInfo.performsNse());
+    }
+    
+    // Handle some special cases first.
+--- rstudio-1.1.463-orig/src/tools/clang-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/clang-ubsan-build	2018-11-17 21:41:02.714507862 +1100
+@@ -10,19 +10,19 @@
+ 
+ : ${RSTUDIO_USE_LIBCXX="Yes"}
+ : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
+-: ${RSTUDIO_BOOST_VERSION="1.56.0"}
++: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.56.0"}
+ 
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp                                                 \
+-    -DLIBR_HOME="${R_HOME}"                                  \
+-    -DCMAKE_C_COMPILER="${CC}"                               \
+-    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
+-    -DCMAKE_CXX_COMPILER="${CXX}"                            \
+-    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
+-    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
+-    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
++cmake ../cpp                                                               \
++    -DLIBR_HOME="${R_HOME}"                                                \
++    -DCMAKE_C_COMPILER="${CC}"                                             \
++    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
++    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
++    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
++    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
++    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
+     "$@"
+ cd ..
+ 
+--- rstudio-1.1.463-orig/src/tools/gcc-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/gcc-ubsan-build	2018-11-17 21:41:02.715507871 +1100
+@@ -19,19 +19,19 @@
+ # NOTE: Boost 1.50.0 not compatible with gcc-6
+ : ${RSTUDIO_USE_LIBCXX="No"}
+ : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
+-: ${RSTUDIO_BOOST_VERSION="1.54.0"}
++: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.54.0"}
+ 
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp                                                 \
+-    -DLIBR_HOME="${R_HOME}"                                  \
+-    -DCMAKE_C_COMPILER="${CC}"                               \
+-    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
+-    -DCMAKE_CXX_COMPILER="${CXX}"                            \
+-    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
+-    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
+-    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
++cmake ../cpp                                                               \
++    -DLIBR_HOME="${R_HOME}"                                                \
++    -DCMAKE_C_COMPILER="${CC}"                                             \
++    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
++    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
++    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
++    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
++    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
+     "$@"
+ cd ..
+ 
+--- rstudio-1.1.463-orig/src/tools/xcode-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/xcode-ubsan-build	2018-11-17 21:41:02.715507871 +1100
+@@ -15,13 +15,13 @@
+ # sanitizers released with newer versions of clang)
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp -GXcode                 \
+-    -DLIBR_HOME="${R_HOME}"          \
+-    -DLIBR_INCLUDE_DIRS="${R_INCL}"  \
+-    -DLIBR_DOC_DIR="${R_DOCS}"       \
+-    -DRSTUDIO_USE_LIBCXX="Yes"       \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="Yes" \
+-    -DRSTUDIO_BOOST_VERSION="1.56.0" \
++cmake ../cpp -GXcode                           \
++    -DLIBR_HOME="${R_HOME}"                    \
++    -DLIBR_INCLUDE_DIRS="${R_INCL}"            \
++    -DLIBR_DOC_DIR="${R_DOCS}"                 \
++    -DRSTUDIO_USE_LIBCXX="Yes"                 \
++    -DRSTUDIO_USE_SYSTEM_BOOST="Yes"           \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="1.56.0" \
+     "$@"
+ cmake ../cpp -DLIBR_LIBRARIES="${R_LIBS}/libR.dylib"
+ cd ..
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
new file mode 100644
index 000000000000..320b823355a3
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
@@ -0,0 +1,46 @@
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-03-30 20:14:40.634057634 +1100
+@@ -296,7 +296,11 @@
+      */
+     timer_ptr set_timer(long duration, timer_handler callback) {
+         timer_ptr new_timer = lib::make_shared<boost::asio::deadline_timer>(
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service,
++#else
+             lib::ref(*m_io_service),
++#endif
+             boost::posix_time::milliseconds(duration)
+         );
+ 
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-03-30 20:14:36.319021594 +1100
+@@ -184,7 +184,12 @@
+         m_io_service = ptr;
+         m_external_io_service = true;
+         m_acceptor = lib::make_shared<boost::asio::ip::tcp::acceptor>(
+-            lib::ref(*m_io_service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service
++#else
++            lib::ref(*m_io_service)
++#endif
++        );
+ 
+         m_state = READY;
+         ec = lib::error_code();
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-03-30 20:15:22.353406097 +1100
+@@ -167,7 +167,12 @@
+         }
+ 
+         m_socket = lib::make_shared<boost::asio::ip::tcp::socket>(
+-            lib::ref(*service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *service
++#else
++            lib::ref(*service)
++#endif
++        );
+ 
+         m_state = READY;
+ 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch
new file mode 100644
index 000000000000..1ec458bb8698
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch
@@ -0,0 +1,46 @@
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-08-20 22:38:53.808923305 +1000
+@@ -296,7 +296,11 @@
+      */
+     timer_ptr set_timer(long duration, timer_handler callback) {
+         timer_ptr new_timer = lib::make_shared<boost::asio::deadline_timer>(
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service,
++#else
+             lib::ref(*m_io_service),
++#endif
+             boost::posix_time::milliseconds(duration)
+         );
+ 
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-08-20 22:38:53.822923358 +1000
+@@ -184,7 +184,12 @@
+         m_io_service = ptr;
+         m_external_io_service = true;
+         m_acceptor = lib::make_shared<boost::asio::ip::tcp::acceptor>(
+-            lib::ref(*m_io_service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service
++#else
++            lib::ref(*m_io_service)
++#endif
++        );
+ 
+         m_state = READY;
+         ec = lib::error_code();
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-08-20 22:38:53.823923362 +1000
+@@ -167,7 +167,12 @@
+         }
+ 
+         m_socket = lib::make_shared<boost::asio::ip::tcp::socket>(
+-            lib::ref(*service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *service
++#else
++            lib::ref(*service)
++#endif
++        );
+ 
+         m_state = READY;
+ 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch
new file mode 100644
index 000000000000..eed2c5c955cb
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch
@@ -0,0 +1,17 @@
+--- rstudio-1.2.1335-orig/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp	2019-04-09 22:08:45.331273559 +1000
+@@ -77,7 +77,13 @@
+       {
+          // start a timer that will cancel any outstanding asynchronous operations
+          // when it elapses if the connection operation has not succeeded
+-         pConnectionTimer_.reset(new boost::asio::deadline_timer(resolver_.get_io_service(), timeout));
++         pConnectionTimer_.reset(new boost::asio::deadline_timer(
++#if BOOST_VERSION >= 107000
++                                   resolver_.get_executor(),
++#else
++                                   resolver_.get_io_service(),
++#endif
++                                   timeout));
+          pConnectionTimer_->async_wait(boost::bind(&TcpIpAsyncConnector::onConnectionTimeout,
+                                                    TcpIpAsyncConnector::shared_from_this(),
+                                                    boost::asio::placeholders::error));
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch
new file mode 100644
index 000000000000..2c4374bb8045
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch
@@ -0,0 +1,160 @@
+--- rstudio-1.2.1335-orig/src/cpp/session/SessionClientInit.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/SessionClientInit.cpp	2019-04-09 18:15:37.746363789 +1000
+@@ -87,13 +87,13 @@
+       boost::shared_ptr<http::Cookie>* pCookie)
+ {
+    // extract the base URL
+-   json::JsonRpcRequest request;
++   core::json::JsonRpcRequest request;
+    Error error = parseJsonRpcRequest(ptrConnection->request().body(), &request);
+    if (error)
+       return error;
+    std::string baseURL;
+ 
+-   error = json::readParams(request.params, &baseURL);
++   error = core::json::readParams(request.params, &baseURL);
+    if (error)
+       return error;
+ 
+@@ -161,7 +161,7 @@
+    }
+ 
+    // prepare session info 
+-   json::Object sessionInfo ;
++   core::json::Object sessionInfo ;
+    sessionInfo["clientId"] = clientId;
+    sessionInfo["mode"] = options.programMode();
+    
+@@ -175,8 +175,8 @@
+    }
+ 
+    // temp dir
+-   FilePath tempDir = rstudio::r::session::utils::tempDir();
+-   Error error = tempDir.ensureDirectory();
++   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
++   core::Error error = tempDir.ensureDirectory();
+    if (error)
+       LOG_ERROR(error);
+    sessionInfo["temp_dir"] = tempDir.absolutePath();
+@@ -194,12 +194,12 @@
+    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
+ 
+    // client state
+-   json::Object clientStateObject;
++   core::json::Object clientStateObject;
+    rstudio::r::session::clientState().currentState(&clientStateObject);
+    sessionInfo["client_state"] = clientStateObject;
+    
+    // source documents
+-   json::Array jsonDocs;
++   core::json::Array jsonDocs;
+    error = modules::source::clientInitDocuments(&jsonDocs);
+    if (error)
+       LOG_ERROR(error);
+@@ -224,7 +224,7 @@
+    if (resumed)
+    {
+       // console actions
+-      json::Object actionsObject;
++     core::json::Object actionsObject;
+       consoleActions.asJson(&actionsObject);
+       sessionInfo["console_actions"] = actionsObject;
+    }
+@@ -290,12 +290,12 @@
+    }
+    else
+    {
+-      sessionInfo["active_project_file"] = json::Value();
+-      sessionInfo["project_ui_prefs"] = json::Value();
+-      sessionInfo["project_open_docs"] = json::Value();
++      sessionInfo["active_project_file"] = core::json::Value();
++      sessionInfo["project_ui_prefs"] = core::json::Value();
++      sessionInfo["project_open_docs"] = core::json::Value();
+       sessionInfo["project_supports_sharing"] = false;
+       sessionInfo["project_owned_by_user"] = false;
+-      sessionInfo["project_user_data_directory"] = json::Value();
++      sessionInfo["project_user_data_directory"] = core::json::Value();
+    }
+ 
+    sessionInfo["system_encoding"] = std::string(::locale2charset(NULL));
+@@ -332,20 +332,20 @@
+       sessionInfo["build_tools_bookdown_website"] =
+                               module_context::isBookdownWebsite();
+ 
+-      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
++      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+       if (!buildTargetDir.empty())
+       {
+          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
+                                                                 buildTargetDir);
+-         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
++         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
+                                       buildTargetDir.childPath("src").exists();
+          sessionInfo["has_pkg_vig"] =
+-               (type == r_util::kBuildTypePackage) &&
++               (type == core::r_util::kBuildTypePackage) &&
+                buildTargetDir.childPath("vignettes").exists();
+       }
+       else
+       {
+-         sessionInfo["build_target_dir"] = json::Value();
++         sessionInfo["build_target_dir"] = core::json::Value();
+          sessionInfo["has_pkg_src"] = false;
+          sessionInfo["has_pkg_vig"] = false;
+       }
+@@ -353,9 +353,9 @@
+    }
+    else
+    {
+-      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
++      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
+       sessionInfo["build_tools_bookdown_website"] = false;
+-      sessionInfo["build_target_dir"] = json::Value();
++      sessionInfo["build_target_dir"] = core::json::Value();
+       sessionInfo["has_pkg_src"] = false;
+       sessionInfo["has_pkg_vig"] = false;
+    }
+@@ -364,7 +364,7 @@
+    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
+ 
+    sessionInfo["tutorial_api_available"] = false;
+-   sessionInfo["tutorial_api_client_origin"] = json::Value();
++   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
+ 
+    sessionInfo["build_state"] = modules::build::buildStateAsJson();
+    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
+@@ -375,7 +375,7 @@
+ 
+    // console history -- we do this at the end because
+    // restoreBuildRestartContext may have reset it
+-   json::Array historyArray;
++   core::json::Array historyArray;
+    rstudio::r::session::consoleHistory().asJson(&historyArray);
+    sessionInfo["console_history"] = historyArray;
+    sessionInfo["console_history_capacity"] =
+@@ -447,14 +447,14 @@
+ 
+    sessionInfo["multi_session"] = options.multiSession();
+ 
+-   json::Object rVersionsJson;
++   core::json::Object rVersionsJson;
+    rVersionsJson["r_version"] = module_context::rVersion();
+    rVersionsJson["r_version_label"] = module_context::rVersionLabel();
+    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
+    sessionInfo["r_versions_info"] = rVersionsJson;
+ 
+    sessionInfo["show_user_home_page"] = options.showUserHomePage();
+-   sessionInfo["user_home_page_url"] = json::Value();
++   sessionInfo["user_home_page_url"] = core::json::Value();
+    
+    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
+    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
+@@ -491,7 +491,7 @@
+ 
+    // create response  (we always set kEventsPending to false so that the client
+    // won't poll for events until it is ready)
+-   json::JsonRpcResponse jsonRpcResponse;
++   core::json::JsonRpcResponse jsonRpcResponse;
+    jsonRpcResponse.setField(kEventsPending, "false");
+    jsonRpcResponse.setResult(sessionInfo);
+ 
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
new file mode 100644
index 000000000000..e38f5e0c4448
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
@@ -0,0 +1,13 @@
+--- rstudio-1.2.1335-orig/src/cpp/server_core/SecureKeyFile.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server_core/SecureKeyFile.cpp	2019-04-09 20:47:57.943317208 +1000
+@@ -68,8 +68,8 @@
+          return error;
+ 
+       // change mode it so it is only readable and writeable by this user
+-      if (changeFileMode(secureKeyPath,
+-                         core::system::UserReadWriteMode) < 0)
++      if (!!changeFileMode(secureKeyPath,
++                           core::system::UserReadWriteMode))
+       {
+          return systemError(errno, ERROR_LOCATION);
+       }
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch
new file mode 100644
index 000000000000..e07ead68969e
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch
@@ -0,0 +1,11 @@
+--- rstudio-1.2.1335-orig/src/cpp/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/CMakeLists.txt	2019-04-09 17:58:59.926559001 +1000
+@@ -117,7 +117,7 @@
+          add_definitions(-O0)
+          add_definitions(-D_GLIBCXX_ASSERTIONS)
+       endif()
+-      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pie -Wl,-z,relro,-z,now")
++      set(CMAKE_EXE_LINKER_FLAGS "-pie -Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
+    endif()
+ 
+    # other useful gcc diagnostics
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
new file mode 100644
index 000000000000..e2fe83867bcd
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
@@ -0,0 +1,32 @@
+--- rstudio-1.2.1335-orig/src/cpp/session/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/CMakeLists.txt	2019-04-09 17:22:59.210201624 +1000
+@@ -25,9 +25,6 @@
+ if(NOT EXISTS "${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
+ 
+@@ -479,19 +476,6 @@
+ install(DIRECTORY "resources/connections"
+         DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-# install pandoc
+-if(WIN32)
+-   set(PANDOC_VERSION "2.6" CACHE INTERNAL "Pandoc version")
+-else()
+-   set(PANDOC_VERSION "2.3.1" CACHE INTERNAL "Pandoc version")
+-endif()
+-
+-set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
+-file(GLOB PANDOC_FILES "${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-1.2.1335-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
new file mode 100644
index 000000000000..ba66ef9f0ea1
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
@@ -0,0 +1,118 @@
+--- rstudio-1.2.1335-orig/CMakeGlobals.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/CMakeGlobals.txt	2019-04-09 17:10:07.680657631 +1000
+@@ -161,7 +161,7 @@
+    set(RSTUDIO_INSTALL_SUPPORTING RStudio.app/Contents/Resources)
+ else()
+    set(RSTUDIO_INSTALL_BIN bin)
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.2.1335-orig/src/cpp/server/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server/CMakeLists.txt	2019-04-09 16:54:34.740739744 +1000
+@@ -194,7 +194,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -202,7 +202,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -210,13 +210,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -224,12 +224,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-1.2.1335-orig/src/cpp/server/ServerOptions.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server/ServerOptions.cpp	2019-04-09 16:54:34.740739744 +1000
+@@ -389,8 +389,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.2.1335-orig/src/cpp/session/SessionOptions.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/SessionOptions.cpp	2019-04-09 17:17:06.035206050 +1000
+@@ -53,7 +53,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ 
+@@ -569,14 +569,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -601,7 +601,7 @@
+    }
+    winptyPath_ = pty.complete(completion).absolutePath();
+ #endif // _WIN32
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
new file mode 100644
index 000000000000..e72df553eeb6
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
@@ -0,0 +1,53 @@
+--- rstudio-1.2.1335-orig/src/gwt/build.xml	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/gwt/build.xml	2019-04-09 16:44:15.089471934 +1000
+@@ -34,6 +34,7 @@
+    <property name="gwt.extra.args" value=""/>
+    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+    <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <path id="project.class.path">
+      <pathelement location="${build.dir}"/>
+@@ -112,8 +113,10 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
+          <jvmarg value="-Xmx1536M"/>
++         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
+          <arg value="-war"/>
+          <arg value="${www.dir}"/>
+          <arg value="-localWorkers"/>
+@@ -154,6 +157,7 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -176,6 +180,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -202,6 +207,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+       	<arg value="-src"/>
+       	<arg value = "src"/>
+@@ -237,6 +243,7 @@
+             <pathelement location="${test.dir}"/>
+             <pathelement location="${src.dir}"/>
+         </classpath>
++        <jvmarg value="-Duser.home=${env.T}"/>
+         <classpath refid="project.class.path"/>
+         <classpath refid="unittest.class.path"/>
+         <arg value="org.rstudio.studio.client.RStudioUnitTestSuite"/>
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch
new file mode 100644
index 000000000000..a59fa02f1d2c
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch
@@ -0,0 +1,60 @@
+--- rstudio-1.2.1335-orig/src/cpp/desktop/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/desktop/CMakeLists.txt	2019-04-09 18:04:57.783616412 +1000
+@@ -140,6 +140,13 @@
+ get_filename_component(QT_LIBRARY_PATH "${QT_BIN_DIR}/../lib"     ABSOLUTE CACHE)
+ get_filename_component(QT_INSTALL_PATH "${QT_BIN_DIR}/.."         ABSOLUTE CACHE)
+ 
++find_path(QTSINGLEAPPLIB_INCLUDE_DIR NAMES QtSingleApplication
++  PATH_SUFFIXES QtSolutions
++  PATHS
++  /usr/include/qt5)
++find_library(QTSINGLEAPPLIB Qt5Solutions_SingleApplication-2.6
++  libQt5Solutions_SingleApplication-2.6)
++
+ # disable clang warnings for qt sources
+ if(APPLE)
+    add_definitions(-Wno-unused-private-field
+@@ -158,7 +165,6 @@
+ 
+ set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
+ list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
+-  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/qtsingleapplication/qtlockedfile.h
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
+@@ -224,8 +230,6 @@
+   DesktopSlotBinders.cpp
+   DesktopSubMenu.cpp
+   DesktopSynctex.cpp
+-  3rdparty/qtsingleapplication/qtsingleapplication.cpp
+-  3rdparty/qtsingleapplication/qtlocalpeer.cpp
+ )
+ 
+ if(WIN32)
+@@ -280,6 +284,7 @@
+   ${CORE_SOURCE_DIR}/include
+   ${CMAKE_CURRENT_SOURCE_DIR}
+   ${CMAKE_CURRENT_BINARY_DIR}
++  ${QTSINGLEAPPLIB_INCLUDE_DIR}
+   ${TESTS_INCLUDE_DIR}
+ )
+ 
+@@ -384,6 +389,7 @@
+    # set link dependencies
+    target_link_libraries(rstudio
+       ${RSTUDIO_QTMODULES}
++      ${QTSINGLEAPPLIB}
+       ${QT_LIBRARIES}
+       ${Boost_LIBRARIES}
+       rstudio-core
+--- rstudio-1.2.1335-orig/src/cpp/desktop/DesktopPosixApplication.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/desktop/DesktopPosixApplication.hpp	2019-04-09 18:01:39.333920927 +1000
+@@ -16,7 +16,7 @@
+ #ifndef DESKTOP_POSIX_APPLICATION_HPP
+ #define DESKTOP_POSIX_APPLICATION_HPP
+ 
+-#include "3rdparty/qtsingleapplication/QtSingleApplication"
++#include <QtSingleApplication>
+ 
+ #include "DesktopApplicationLaunch.hpp"
+ 
diff --git a/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
new file mode 100644
index 000000000000..cc1c95318e3a
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
@@ -0,0 +1,255 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+PANDOC_VER=1.19.2.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${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_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.4
+	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 )
+	!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}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+		"${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch"
+		"${FILESDIR}/${PN}-1.1.453-core.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p3.patch"
+		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.70.0.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_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${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:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${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 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+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_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 "${FILESDIR}"/rsession.conf
+	dosym "${EROOT}/etc/conf.d/rstudio-server.conf" "/etc/rstudio/rserver.conf"
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+}
diff --git a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
index 271588e60b84..5c0511bb9a52 100644
--- a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
@@ -101,6 +101,7 @@ PATCHES=(
 		"${FILESDIR}/${PN}-1.1.453-core.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p3.patch"
 		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
 )
 
diff --git a/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild b/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
new file mode 100644
index 000000000000..60a61cb90a35
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
@@ -0,0 +1,253 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils user cmake-utils gnome2-utils pam 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=2.8.1
+GIN_VER=2.1.2
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+# It should be PANDOC_VER=2.3.1 however >=app-text/pandoc-2.3.1 is not yet in portage
+PANDOC_VER=1.19.2.1
+# 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_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.4
+	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/qtwebengine-${QT_VER}:${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 )
+	!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}/${PN}-1.2.1335-prefs.patch"
+		"${FILESDIR}/${PN}-1.2.1335-paths.patch"
+		"${FILESDIR}/${PN}-1.2.1335-pandoc.patch"
+		"${FILESDIR}/${PN}-1.2.1335-linker_flags.patch"
+		"${FILESDIR}/${PN}-1.2.1335-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+		"${FILESDIR}/${PN}-1.2.1335-core.patch"
+		"${FILESDIR}/${PN}-1.2.1335-fix-ptr-int-compare.patch"
+		"${FILESDIR}/${PN}-1.2.1335-boost-1.70.0_p1.patch"
+		"${FILESDIR}/${PN}-1.2.1335-boost-1.70.0_p2.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_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${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:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${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 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+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_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 "${FILESDIR}"/rsession.conf
+	dosym "${ED}/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 || { 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 ;}
+}
diff --git a/sci-mathematics/spass/Manifest b/sci-mathematics/spass/Manifest
index fe06a9388497..3f6eac8e73fd 100644
--- a/sci-mathematics/spass/Manifest
+++ b/sci-mathematics/spass/Manifest
@@ -1,5 +1,3 @@
-DIST spass37.tgz 1340925 BLAKE2B 5b71778702f61a62e1ec6bd6136fb53ab50f746cab9437510a22141702384b425502c321651910f881c908d0d5640a223ae632e2e0c0f9dbd347cd7ee5c435f6 SHA512 5b4efd7b767dfee3f24e7917a6ec58ac240ab33bf601722eabd50af57637d8fdd62de9e34e7cd1cd98b8b7e371c9e2d47c8fa3e07c6e7ce2fa616a76646a4e12
 DIST spass39.tgz 554633 BLAKE2B ca2215f205215805eace6abae82ad281bdadd75f2a52cfe3fed43cb15a4955a4e4d2375fc73a546592315540a7596494bc0df4c53996fd9299e901f68a81ddc8 SHA512 d7ea0697426c476f2e03b2f9078b7e060671067a67fad7144bb5887a2dd3f39e19e1888f121fce546b5d6ea9a4dc458d1cbec56b59c93507e7dc2d0afa25a89b
-EBUILD spass-3.7.ebuild 1991 BLAKE2B db0b3f9a499dadfa94d30838fcf59fa35f2cb463501502448e5301cb0532efdac20a9131960e85d0cd12cb8abd2dbd5a2a8721a107b4906b9d051aaa3271a562 SHA512 a155b205249cd9e80b274d8316d42e3a69d60aeecaabe4162b8b6225433a138b5b33605cde7dea391b65c9acb97f65807e0bbf7f2eb9fbe7970e38c81cccb33b
-EBUILD spass-3.9.ebuild 4528 BLAKE2B 4004195f26de851c50a4d0d9631bf08fa808a45db3efb2421823097bceda8da062c048020bb84b187d4bdbcfdea74e641226935150dfc105cf698a7949f9f977 SHA512 5cd41de9201063f2ebf696b5cdd1cf2572e6e0e99282c41a0fd3a92ea8589337da63e4392e0e45257b79dd667d986f7206655310696372ce433e43f5473a6f2c
+EBUILD spass-3.9.ebuild 4528 BLAKE2B cde0847e8e2779971f33c1901f4601083c7490082d987a3286c89b1b7c72b8f5c5824aa3762f3eab99b4748c17f0cc6e38bd6f5ced7cf66ff87e4a013b6349a0 SHA512 e00e0c0a2fe8ffc3b5e5ff193a90ed002ffb0a7173cd31837351d32e86201b4bb0296ee49e203ebba9b67f948448f93e3f8acd317f1f800691d6b8a9ed3b0a2f
 MISC metadata.xml 577 BLAKE2B 7d0a60f31459c0a514ae829d1a56efdb55ac0abb5c5202e1e8400755ae4593ef183e9770e2308545af2b17ad7e385d15c48a9ee630a3cd20d1feb5f0edc189d1 SHA512 7cd50f06b202828fd682e2f44d361b393cc89f0468001970c2ad807e26d7fa5399cba09e6805a937cfba9c56019b67ab3dec422a989e16cbb5216fa76c253285
diff --git a/sci-mathematics/spass/spass-3.7.ebuild b/sci-mathematics/spass/spass-3.7.ebuild
deleted file mode 100644
index 6f16128d8a8c..000000000000
--- a/sci-mathematics/spass/spass-3.7.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit versionator
-
-MY_PV=$(delete_all_version_separators "${PV}")
-MY_P="${PN}${MY_PV}"
-
-DESCRIPTION="An Automated Theorem Prover for First-Order Logic with Equality"
-HOMEPAGE="http://www.spass-prover.org/"
-SRC_URI="http://www.spass-prover.org/download/sources/${MY_P}.tgz"
-
-LICENSE="BSD-2"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples isabelle"
-
-RDEPEND="isabelle? (
-			>=sci-mathematics/isabelle-2011.1-r1:=
-		)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/SPASS-${PV}"
-
-src_prepare() {
-	sed \
-		-e "s:-O3:${CFLAGS}:g" \
-		-i configure || die
-}
-
-src_install() {
-	default
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	if use isabelle; then
-		ewarn "All open source versions of spass are broken with Isabelle 2016.1"
-		ISABELLE_HOME="$(isabelle getenv ISABELLE_HOME | cut -d'=' -f 2)"
-		[[ -n "${ISABELLE_HOME}" ]] || die "ISABELLE_HOME empty"
-		dodir "${ISABELLE_HOME}/contrib/${PN}-${PV}/etc"
-		cat <<- EOF >> "${S}/settings"
-			SPASS_HOME="${ROOT}usr/bin"
-			SPASS_VERSION="${PV}"
-		EOF
-		insinto "${ISABELLE_HOME}/contrib/${PN}-${PV}/etc"
-		doins "${S}/settings"
-	fi
-}
-
-pkg_postinst() {
-	if use isabelle; then
-		if [ -f "${ROOT}etc/isabelle/components" ]; then
-			if egrep "contrib/${PN}-[0-9.]*" "${ROOT}etc/isabelle/components"; then
-				sed -e "/contrib\/${PN}-[0-9.]*/d" \
-					-i "${ROOT}etc/isabelle/components"
-			fi
-			cat <<- EOF >> "${ROOT}etc/isabelle/components"
-				contrib/${PN}-${PV}
-			EOF
-		fi
-	fi
-}
-
-pkg_postrm() {
-	if use isabelle; then
-		if [ ! -f "${ROOT}usr/bin/SPASS" ]; then
-			if [ -f "${ROOT}etc/isabelle/components" ]; then
-				# Note: this sed should only match the version of this ebuild
-				# Which is what we want as we do not want to remove the line
-				# of a new spass being installed during an upgrade.
-				sed -e "/contrib\/${PN}-${PV}/d" \
-					-i "${ROOT}etc/isabelle/components"
-			fi
-		fi
-	fi
-}
diff --git a/sci-mathematics/spass/spass-3.9.ebuild b/sci-mathematics/spass/spass-3.9.ebuild
index 8fdbb7ebb633..c702deaec240 100644
--- a/sci-mathematics/spass/spass-3.9.ebuild
+++ b/sci-mathematics/spass/spass-3.9.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit versionator
+inherit toolchain-funcs
 
-MY_PV=$(delete_all_version_separators "${PV}")
+MY_PV=$(ver_rs 1- '' "${PV}")
 MY_P="${PN}${MY_PV}"
 
 DESCRIPTION="An Automated Theorem Prover for First-Order Logic with Equality"
@@ -108,7 +108,7 @@ src_install() {
 		[[ -n "${ISABELLE_HOME}" ]] || die "ISABELLE_HOME empty"
 		dodir "${ISABELLE_HOME}/contrib/${PN}-${PV}/etc"
 		cat <<- EOF >> "${S}/settings"
-			SPASS_HOME="${ROOT}usr/bin"
+			SPASS_HOME="${EROOT}/usr/bin"
 			SPASS_VERSION="${PV}"
 		EOF
 		insinto "${ISABELLE_HOME}/contrib/${PN}-${PV}/etc"
@@ -118,12 +118,12 @@ src_install() {
 
 pkg_postinst() {
 	if use isabelle; then
-		if [ -f "${ROOT}etc/isabelle/components" ]; then
-			if egrep "contrib/${PN}-[0-9.]*" "${ROOT}etc/isabelle/components"; then
+		if [ -f "${EROOT}/etc/isabelle/components" ]; then
+			if egrep "contrib/${PN}-[0-9.]*" "${EROOT}/etc/isabelle/components"; then
 				sed -e "/contrib\/${PN}-[0-9.]*/d" \
-					-i "${ROOT}etc/isabelle/components"
+					-i "${EROOT}/etc/isabelle/components"
 			fi
-			cat <<- EOF >> "${ROOT}etc/isabelle/components"
+			cat <<- EOF >> "${EROOT}/etc/isabelle/components"
 				contrib/${PN}-${PV}
 			EOF
 		fi
@@ -132,13 +132,13 @@ pkg_postinst() {
 
 pkg_postrm() {
 	if use isabelle; then
-		if [ ! -f "${ROOT}usr/bin/SPASS" ]; then
-			if [ -f "${ROOT}etc/isabelle/components" ]; then
+		if [ ! -f "${EROOT}/usr/bin/SPASS" ]; then
+			if [ -f "${EROOT}/etc/isabelle/components" ]; then
 				# Note: this sed should only match the version of this ebuild
 				# Which is what we want as we do not want to remove the line
 				# of a new spass being installed during an upgrade.
 				sed -e "/contrib\/${PN}-${PV}/d" \
-					-i "${ROOT}etc/isabelle/components"
+					-i "${EROOT}/etc/isabelle/components"
 			fi
 		fi
 	fi
author	V3n3RiX <venerix@redcorelinux.org>	2019-09-06 10:28:05 +0100
committer	V3n3RiX <venerix@redcorelinux.org>	2019-09-06 10:28:05 +0100
commit	f1af93971b7490792d8541bc790e0d8c6d787059 (patch)
tree	a38046712bbc3a3844d77452d16c84e716caa3d4 /sci-mathematics
parent	fc637fb28da700da71ec2064d65ca5a7a31b9c6c (diff)