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authorV3n3RiX <venerix@redcorelinux.org>2020-05-30 11:44:06 +0100
committerV3n3RiX <venerix@redcorelinux.org>2020-05-30 11:44:06 +0100
commitf516638b7fe9592837389826a6152a7e1b251c54 (patch)
tree8bfecb640b7b6403d7a3d662d923eed630033da7 /sci-mathematics
parent1a61119f9f7b057830e2ce0563f913ec86f282ad (diff)
gentoo resync : 30.05.2020
Diffstat (limited to 'sci-mathematics')
-rw-r--r--sci-mathematics/Manifest.gzbin13507 -> 13670 bytes
-rw-r--r--sci-mathematics/agda-lib-ffi/Manifest4
-rw-r--r--sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2-r2.ebuild4
-rw-r--r--sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2.ebuild6
-rw-r--r--sci-mathematics/agda-stdlib/Manifest4
-rw-r--r--sci-mathematics/agda-stdlib/agda-stdlib-2.4.2.5.ebuild4
-rw-r--r--sci-mathematics/agda-stdlib/agda-stdlib-2.5.2.0.13.ebuild4
-rw-r--r--sci-mathematics/agda/Manifest6
-rw-r--r--sci-mathematics/agda/agda-2.4.2.5-r2.ebuild4
-rw-r--r--sci-mathematics/agda/agda-2.5.2-r1.ebuild4
-rw-r--r--sci-mathematics/agda/agda-2.5.2-r2.ebuild4
-rw-r--r--sci-mathematics/alt-ergo/Manifest2
-rw-r--r--sci-mathematics/alt-ergo/alt-ergo-2.3.0.ebuild9
-rw-r--r--sci-mathematics/gimps/Manifest2
-rw-r--r--sci-mathematics/gimps/gimps-29.8.6-r1.ebuild (renamed from sci-mathematics/gimps/gimps-29.8.6.ebuild)3
-rw-r--r--sci-mathematics/mathmod/Manifest2
-rw-r--r--sci-mathematics/mathmod/mathmod-4.1-r1.ebuild22
-rw-r--r--sci-mathematics/octave/Manifest2
-rw-r--r--sci-mathematics/octave/octave-5.2.0.ebuild2
-rw-r--r--sci-mathematics/psmt2-frontend/Manifest2
-rw-r--r--sci-mathematics/psmt2-frontend/psmt2-frontend-0.2.ebuild11
-rw-r--r--sci-mathematics/pymc3/Manifest2
-rw-r--r--sci-mathematics/pymc3/pymc3-3.1-r1.ebuild (renamed from sci-mathematics/pymc3/pymc3-3.1.ebuild)2
-rw-r--r--sci-mathematics/rkward/Manifest4
-rw-r--r--sci-mathematics/rkward/rkward-0.7.1b.ebuild (renamed from sci-mathematics/rkward/rkward-0.7.1.ebuild)2
-rw-r--r--sci-mathematics/rstudio/Manifest45
-rw-r--r--sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch18
-rw-r--r--sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch45
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch130
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch76
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch38
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch460
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch220
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch167
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch46
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch13
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch31
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch13
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch32
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch53
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.2.5042-R-4.0.0.patch106
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch106
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch (renamed from sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch)89
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch42
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch (renamed from sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch)64
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch68
-rw-r--r--sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch (renamed from sci-mathematics/rstudio/files/rstudio-0.99.473-qtsingleapplication.patch)44
-rw-r--r--sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild255
-rw-r--r--sci-mathematics/rstudio/rstudio-1.2.5033.ebuild3
-rw-r--r--sci-mathematics/rstudio/rstudio-1.2.5042.ebuild2
-rw-r--r--sci-mathematics/rstudio/rstudio-1.3.959.ebuild (renamed from sci-mathematics/rstudio/rstudio-1.2.1335.ebuild)131
-rw-r--r--sci-mathematics/rw/Manifest1
-rw-r--r--sci-mathematics/rw/rw-0.8-r3.ebuild40
-rw-r--r--sci-mathematics/sympow/Manifest5
-rw-r--r--sci-mathematics/sympow/files/sympow-2.023.6-dont-force-O3.patch53
-rw-r--r--sci-mathematics/sympow/files/sympow-2.023.6-no-pkgdatafilesbindir-warnings.patch45
-rw-r--r--sci-mathematics/sympow/metadata.xml24
-rw-r--r--sci-mathematics/sympow/sympow-2.023.6.ebuild45
-rw-r--r--sci-mathematics/why3-for-spark/Manifest2
-rw-r--r--sci-mathematics/why3-for-spark/files/why3-for-spark-2019-gentoo.patch10
-rw-r--r--sci-mathematics/wxmaxima/Manifest2
-rw-r--r--sci-mathematics/wxmaxima/wxmaxima-20.04.0.ebuild49
62 files changed, 850 insertions, 1834 deletions
diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index 83981adfa0fe..2c9f78ca9162 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
Binary files differ
diff --git a/sci-mathematics/agda-lib-ffi/Manifest b/sci-mathematics/agda-lib-ffi/Manifest
index a507a1945291..177f83a141d9 100644
--- a/sci-mathematics/agda-lib-ffi/Manifest
+++ b/sci-mathematics/agda-lib-ffi/Manifest
@@ -1,5 +1,5 @@
DIST agda-stdlib-2.4.2.3.tar.gz 252558 BLAKE2B 2373b9d395a64fe7f23bbb583d8cfc5b2572f5aa3ea98b687e8f122ae1accae835e4ed1ebfe7252a5bc5e519898b9ca39e1f19e16bb9f4195246f9904cc2c9af SHA512 d503fc2abd18ab8c367a1947301e0302a6ff9fcbb6376a01f016aa2ab7a9a967e5adb96c5013db1892f4acd9fab62bead11c58c4d443784aff1e42ee4ffd4aa9
DIST lib-0.7.tar.gz 226400 BLAKE2B 4203486fa35d6dbfdcdfa227da43c771e8e2c78d906c06dae8cc3eb473c6ac0029554b98a0a665de80f1d1b5806a82ef68491050b0f90e80065a08ab91dba7c1 SHA512 557aa7b9b143f2e4a2249881a98c753035962bc5d9222241e6b4fe86aab8642986aa9db7ca6fc2b2da8486f9294ff30c4c2edfa0222ba95d9216ed2d0e00c114
-EBUILD agda-lib-ffi-0.0.2-r2.ebuild 733 BLAKE2B 896337f143df0c75aea375969ae9bbc8fac8cce9c821d52a600e4af496897a7304e326141048fdd96327f7fc859c91d77bc66e560710e47765d8925d10f8b17a SHA512 92182ff0f4ff71d3d6f67b2a01dd7a066d21a4c6054b3bd9e4333ed04741b781dc59b8e8e72a5a73b7d3e0e181b93adeb5f3f093ad746a243f38a01bdffdaec1
-EBUILD agda-lib-ffi-0.0.2.ebuild 656 BLAKE2B 89fc97e68ff3067389c6bec6753985b69d167b92b7db05d1cec3235fff426f5f116857b743c843aeaa454e627bb2eb75459535f14a8a49307c4403d9ee7bbcc2 SHA512 08e7debee9a5de4091376447e0aa09186c37878bd745cc6bf96d838f08e442b1b06125fa42c9c9e3e9f4133a4480a8add95fdd69c3938b4807b6238eb7a32140
+EBUILD agda-lib-ffi-0.0.2-r2.ebuild 731 BLAKE2B 84aacabeb83f81b599b457e62d3541c17d2f5e7d5880264a27a560c79a57490666771c602b127e3812fe671dccce21af7f0ea3531b1ad50ac5c90d27821481c1 SHA512 a7870a30ca78b00f3fb4645d394fbbdf881f4e87b189cd590f4587212f1f46dbcb60a73511278305f54768eaf2a4b9d8a52f94d4f2701dc9cfa391f4f1dc724a
+EBUILD agda-lib-ffi-0.0.2.ebuild 655 BLAKE2B cbdf24bdcd0027509b5cee43224f9b1c5e65c4c67263334a683ce848118c05967ebb8751da3742cd90678fe34b8fb06eec77fb33fd9e07f1a8bf02cce91d824e SHA512 ebeed8e5ae98c0a1b2f18bed48cb63cdd8c56d402ee7b61ea513ebd52c1cee744974133dfe3c00a255623c878726f89c871b9a7a94edf2d8406d31e39777a739
MISC metadata.xml 427 BLAKE2B a47c114964a36abbee07f66f13f5af553cbb11bd3e703397ec2650cb13bd23b9971ea0b5dc0692e606efe719b4abfcdc6c3882a091f146c27b173300d753b8ad SHA512 5dcdfd777392fbc8d215e263cf2ef8be706ebb4790bc79f551d19f25bd061a144751b5c4ee39b75cd974fd996239c70a9ca14bcacd512503d0189dec98faf30f
diff --git a/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2-r2.ebuild b/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2-r2.ebuild
index 44bf12e940e8..9f4b8f627c6c 100644
--- a/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2-r2.ebuild
+++ b/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -13,7 +13,7 @@ AGDA_PV="2.4.2.3"
AGDA_P="${AGDA_PN}-${AGDA_PV}"
DESCRIPTION="Auxiliary Haskell code used by Agda's standard library"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://github.com/agda/${AGDA_PN}/archive/${AGDA_PV}.tar.gz -> ${AGDA_P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2.ebuild b/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2.ebuild
index 6b8ed5ad076c..a547e511ba11 100644
--- a/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2.ebuild
+++ b/sci-mathematics/agda-lib-ffi/agda-lib-ffi-0.0.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -11,8 +11,8 @@ inherit haskell-cabal
AGDA_P="lib-0.7"
DESCRIPTION="Auxiliary Haskell code used by Agda's standard library"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
-SRC_URI="http://www.cse.chalmers.se/~nad/software/${AGDA_P}.tar.gz"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
+SRC_URI="https://www.cse.chalmers.se/~nad/software/${AGDA_P}.tar.gz"
LICENSE="MIT"
SLOT="0/${PV}"
diff --git a/sci-mathematics/agda-stdlib/Manifest b/sci-mathematics/agda-stdlib/Manifest
index ebf29755a4bb..fba24e394bbb 100644
--- a/sci-mathematics/agda-stdlib/Manifest
+++ b/sci-mathematics/agda-stdlib/Manifest
@@ -2,6 +2,6 @@ AUX 50agda-stdlib-gentoo.el 58 BLAKE2B e9b9bef913e26c63e4b0e19a1e4b5c0e370959689
AUX standard-library.agda-lib 55 BLAKE2B 057e933b07b291fd505f2e64f43b087c2aa4f4828ba2a03b5a53b9cac0f0fd0ab1f523c91efd6090e34e376dcc61d90bc5193063b6f07280c0eb2d688a07dedc SHA512 b1e2cbffe4b99157661fe6f4685580c7524890735db0a20ae1942e076b00d0df13624f587ea7584319e5665484da63beb3e0e5c77226bdbe02a4a80fa33a17b4
DIST agda-stdlib-2.4.2.5.tar.gz 253379 BLAKE2B c635040892bf940057bacf35f85fa6b7e3b49d1877ca7310933c27312b37566f3df077ad021d34e7855daa1e23b2495df82fe288e8416a11f630beeb313ca027 SHA512 b15ed5838916240c8602fe7a4bccddf43c71ab3a18ecb5a6dc85199b908e261b04cf794a4d93c90af0a9263a36603c392280639ace7fecead0c39269c2623302
DIST agda-stdlib-2.5.2.0.13.tar.gz 264701 BLAKE2B f35b419aac1b80af86217a86fb8e21a2f3427ef9629c8f2e284036859cd89da16ce1b64ceb87f8a3030b5bdb2a68b4f59f74a717fc1e13378ecb20cc6b28f59c SHA512 340a7b9cb15793cdbe99f558a32eaab3476b94b4d43d45bdc92c6b368197d075c977fd2f6ce0c5b0baf584289a2218b07dd030ad2b83f6d9e4bc7effee91eece
-EBUILD agda-stdlib-2.4.2.5.ebuild 1916 BLAKE2B f30b6d5b1eeb31859e0bd6b557fb113fc8ed1eb3dbcfa192b85d8e5cf004b170d5b747a09b81a94125baa457f19abdfbf422b41d24b856ef95a35edc1bb773a5 SHA512 83c74eee1022fda2fcf36346aa3017d3f0a73994037187ef674723ccb90f761c37ed5d75294452d88074e8e44541452edccbc4bf5c3286147f3067923eabbdfa
-EBUILD agda-stdlib-2.5.2.0.13.ebuild 2177 BLAKE2B 9d52c7d2840ffb17bea6d15465d11ea5fdf36c0302009ea4950603bfca8b69ae00b7ba18d12afd02a88964ee8a949c71fd8dc1bbc3be25126ca32fbdfe951245 SHA512 bf10ddd12a01feb400944e0b63d6575dc6c2cfd54f8651f333bb8577e03ef6ce714581dd5ffe077f906746babf65b511df0b1f6e87f5bbf51ce4e6e0e6dcfec5
+EBUILD agda-stdlib-2.4.2.5.ebuild 1914 BLAKE2B f76f7e595d75dcf99b1e6968fd2b1c458e951b1e2807f7110261830cad2b1b436964c826764ec59e5093712dd6ca1b999746b1321a00d902f9e9891bd9ef01cd SHA512 40c9829fe63f6041253dc022c072fc1eca9e8fbdb1945c6d2f89e278cc051df05534397919691b52638a46e656bd6455db185f0dccd1899d581c85be0c6708d2
+EBUILD agda-stdlib-2.5.2.0.13.ebuild 2175 BLAKE2B debbd1f201004b20b3e41ad446eac17e2e5ae53175d2c5c56e1a35e94239835d337f5f87bc9b2f03b39a8b7bc1f52476cf02147f5c47fab5ce9e18aac4086e25 SHA512 18c5b73a3dc72a8ee6839381428f27617d299f7c0f61af6c10ce32279e9d50b43b6a36ae02ed675ee1a196914d7f1a2331318976e038c6fc827ec66f95cc9a23
MISC metadata.xml 658 BLAKE2B 5c799efce1321e2223711ae7626794d6f558fbf40b86b29c3d7bec31c746558e4cbcf1b0040feea20c648a02da876485b7d899afabd416c2dc2a0d302193aea6 SHA512 d1afae7ae946e667e796060d28ef006a47823de3b30c5e493dcba4a606a585b52308e4740b780f88fb7a9b69d1e534bc35514d31b030eed74b6439507e1239c3
diff --git a/sci-mathematics/agda-stdlib/agda-stdlib-2.4.2.5.ebuild b/sci-mathematics/agda-stdlib/agda-stdlib-2.4.2.5.ebuild
index f4be8e1439ec..be6d6baf3910 100644
--- a/sci-mathematics/agda-stdlib/agda-stdlib-2.4.2.5.ebuild
+++ b/sci-mathematics/agda-stdlib/agda-stdlib-2.4.2.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -7,7 +7,7 @@ CABAL_FEATURES="bin"
inherit haskell-cabal elisp-common
DESCRIPTION="Agda standard library"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://github.com/agda/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/agda-stdlib/agda-stdlib-2.5.2.0.13.ebuild b/sci-mathematics/agda-stdlib/agda-stdlib-2.5.2.0.13.ebuild
index e1dcba466e3a..4659c6572de9 100644
--- a/sci-mathematics/agda-stdlib/agda-stdlib-2.5.2.0.13.ebuild
+++ b/sci-mathematics/agda-stdlib/agda-stdlib-2.5.2.0.13.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -18,7 +18,7 @@ MY_GENTOO_AGDA_STDLIB_V="${PV}.${MY_UPSTREAM_AGDA_STDLIB_V}"
MY_UPSTREAM_AGDA_V="${PV%.${MY_UPSTREAM_AGDA_STDLIB_V}}"
DESCRIPTION="Agda standard library"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://github.com/agda/${PN}/archive/v${MY_UPSTREAM_AGDA_STDLIB_V}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/agda/Manifest b/sci-mathematics/agda/Manifest
index 9b3decfc5ba1..7334f7c783c0 100644
--- a/sci-mathematics/agda/Manifest
+++ b/sci-mathematics/agda/Manifest
@@ -2,7 +2,7 @@ AUX 50agda2-gentoo.el 317 BLAKE2B c295509014fc7f254c5c0650b079d3827b182270c6e1aa
AUX agda-2.4.2.5-hashtables.patch 558 BLAKE2B 88532103f488b643ac84ad37fae3776514034121624c43610910c44a67ac0e68cc5d5d8afece38e2fbf95dbaa3e268e2418d1c34ba4a8fbc60637d63765be42d SHA512 0297fc4605db3dc11f08ec068cfdce908d273c6d14f472e4d00b4416a8e5f671b3b77d4e0cb671671bafd07b39ec46e72eab6cab972145199b25b3c4cfb0b3a6
DIST Agda-2.4.2.5.tar.gz 1031427 BLAKE2B bf64731e0c068c4f609e9651f0cb6ea763f1e02ddd8909269a140f8ebd036dbb5b36d9f1b038a32016447bbfbd4f9dd6a00a1cc34616efd7099a2b4ddcc7d3bc SHA512 c2e090a42f699200854c20dad868b4b67e99107f0cdbba20ed268f4618fcf80068ee31db37e4b6637f73128d9f652ef9276d8f7adea54628da759d79f5e4f4a2
DIST Agda-2.5.2.tar.gz 1240885 BLAKE2B bccdaa0c40b8e116f44ee436171cec0a8e1366d7b1f0b469bf459eacf4256e29a00c60a371dcf7971c499e948ce6264861016bb51fcad3251f62cb3e7370c19c SHA512 39ec73316eb7409f7f2618e86a9a3a2c420c93470bf46a1c37a4c4753c6c831d2d6da9ba007086ddee9defd481a695bf142a0a7d360dfa01bdb1fb92467af164
-EBUILD agda-2.4.2.5-r2.ebuild 4435 BLAKE2B 23391332d6a47ef08ded30dacafeaadaf90b7952f955370edbed5433e65fa9d589cf3aa5efedba072d936fbed19ac69fb7859ac559cbb50da87c1724479c3505 SHA512 4820821774519193231316539eb749f99a72c0bac66635c9498f91f68dcdd4899d6082c2d40b0a212de505ecada4ecf35b7e726e7279490a9a05699b028920f1
-EBUILD agda-2.5.2-r1.ebuild 5269 BLAKE2B dc51c050ba5a34cdcd4b47914fc0bd6eab1831598874b1d9aa388cdfdfd4c9fb09bec0c60e60abeb050e5a688571ba5d466066124be7044b3d4bee841d3ec6ab SHA512 b18c10ec2c8fdcc6f861c7fb06bc8459edb430cec90ee0b2ffaa139bab0be245ff328ee88289dcb73786bc269036af9c373c7bda212c0dbd54d1113697c0e407
-EBUILD agda-2.5.2-r2.ebuild 5304 BLAKE2B c8b634ef9ba0c757503364ac267792b001b1a62c698450a30ea8874d6adb3740151ca3acf4446753460ff0601217cea4cdce4aa48a75bfd9cd0b8f08f4795218 SHA512 955943813bc8538426e09d9bd506dbc1a09d72fe229a5d1365007751f28d1c2e038c2bcaf587a0a490233b1dc1024abbbfc9408655900764c91c1e57f61ff4a3
+EBUILD agda-2.4.2.5-r2.ebuild 4436 BLAKE2B 95e7429fdf3b03505aa2357e2ff7da7b9246d371cf595a26ef9d05dc23d42f4b1267a4cc3759a89ecd135e77ce390fc9db8ed333591159286dae6f594f8931b7 SHA512 8a0f546dc68745851a8083db3a8dff1e141b727026be86ab207ce848500553964cea1c3ca16ef4ffb3492cc13011ccddd50b03fe7dc63723a6f43730d97c075b
+EBUILD agda-2.5.2-r1.ebuild 5270 BLAKE2B fadb3f989c59b25c576376534c43b16d896f99d6cfb349c9ec59364428eec21651943e5a71daf6951aedda6fe8bc97b031b670652dae66ff954dca20fbcb070d SHA512 9de1a2016cdb763df7e450c80514417f3cff228fe97b3a2f7041722b3a09904c99a24e5c152bba54ea10c28b8c37c2b2ac2a5f1a68ef00d38e8335f93159332d
+EBUILD agda-2.5.2-r2.ebuild 5305 BLAKE2B b5fe5d674d023921cc3a6e3a13d281d3289306f0d7ad08b0f1402fdabff79d8ae7a58ac9a17437fa298d142ee601b02256222bfdbec8994d687ad61522b16e65 SHA512 faa7262d365ebdfb1d3b19e4ee2c1a7b8d4e02d91fb414fba5fedee4da92e6027690fa00e6fc92714e22920f43753d059e79841cebafc6bc2ef8e2f3fa77090c
MISC metadata.xml 907 BLAKE2B f4890d2c0e7c8d3eeb57ad9472ae3b5ae287fc7880fa853ec5d1a6c9867aa3e11ef71cd5b46ed5e9fd9e3c3307eea1260c4aa0d9f1598de64f48f43e0c2af137 SHA512 d48af119f929e739634165e1ece14ef2bf55eb996fd0852fd34783a18da04a156bf858b3f0a7ad3cd5c85e55c564bfb3e5552786161fd2ad66f86eb5d3d91426
diff --git a/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild b/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
index 634862b133ad..63b99d3e1cba 100644
--- a/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
+++ b/sci-mathematics/agda/agda-2.4.2.5-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -12,7 +12,7 @@ MY_PN="Agda"
MY_P="${MY_PN}-${PV}"
DESCRIPTION="A dependently typed functional programming language and proof assistant"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://hackage.haskell.org/package/${MY_P}/${MY_P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/agda/agda-2.5.2-r1.ebuild b/sci-mathematics/agda/agda-2.5.2-r1.ebuild
index 9bc509d3579c..1c7e55a7ad8d 100644
--- a/sci-mathematics/agda/agda-2.5.2-r1.ebuild
+++ b/sci-mathematics/agda/agda-2.5.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -22,7 +22,7 @@ MY_UPSTREAM_AGDA_STDLIB_V="0.13"
MY_GENTOO_AGDA_STDLIB_V="${PV}.${MY_UPSTREAM_AGDA_STDLIB_V}"
DESCRIPTION="A dependently typed functional programming language and proof assistant"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://hackage.haskell.org/package/${MY_P}/${MY_P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/agda/agda-2.5.2-r2.ebuild b/sci-mathematics/agda/agda-2.5.2-r2.ebuild
index c5ee1f841665..620d6ba28f88 100644
--- a/sci-mathematics/agda/agda-2.5.2-r2.ebuild
+++ b/sci-mathematics/agda/agda-2.5.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -22,7 +22,7 @@ MY_UPSTREAM_AGDA_STDLIB_V="0.13"
MY_GENTOO_AGDA_STDLIB_V="${PV}.${MY_UPSTREAM_AGDA_STDLIB_V}"
DESCRIPTION="A dependently typed functional programming language and proof assistant"
-HOMEPAGE="http://wiki.portal.chalmers.se/agda/"
+HOMEPAGE="https://wiki.portal.chalmers.se/agda/"
SRC_URI="https://hackage.haskell.org/package/${MY_P}/${MY_P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-mathematics/alt-ergo/Manifest b/sci-mathematics/alt-ergo/Manifest
index 4d4f8cf75741..48d3a95257ff 100644
--- a/sci-mathematics/alt-ergo/Manifest
+++ b/sci-mathematics/alt-ergo/Manifest
@@ -1,5 +1,5 @@
DIST alt-ergo-1.30.tar.gz 380329 BLAKE2B fab16757ed110474cf8f9d01ab53f76b6a300eb478b32bbfd6bb79d7603b1f5c2fc5c97bf44358eb138283f3487ef90febd23865723a4721b01bd870cfdd6507 SHA512 6ac6abdc6602b0ba89ee58eb96c66ac93e8195e0b4f75595381eded86365c2dd881251de2b77e2f1137684651ddc7fd94f922509de0be2964d81f52a6fb0f2f2
DIST alt-ergo-2.3.0.tar.gz 455577 BLAKE2B 1836782be452df5147fc3041517fd267f3ce7facd15ad460c3e1dfba2b6ea455fee79ad8264ccb12cf21622c21a54c186c9943e7bffb392daab15d046ff93863 SHA512 a2f209b62b8494bfefe84328cdc786185e0534c5e224e212b83045b078352a51d2ab02622f72c22c74c7de95c7a554cbdae2a9a8a0c41f3f26c841f8c72f6b21
EBUILD alt-ergo-1.30.ebuild 705 BLAKE2B 2ed4bdb55ba084ae8364cf49200a61b9b4c64941817acc1a448ebb5124eaaac264c8d895e5d98e4093fca05a9b7d6db638cf89a808d95af313c49a79cc94f9b9 SHA512 aa1f48cb7fb8d99d7745d77edbc9f69f9f591029c354018243d309f6d27be7e595758ae2f46a7854e82b456afc5405205e31d5f84e974949ad6e9248dc48cd39
-EBUILD alt-ergo-2.3.0.ebuild 1063 BLAKE2B 3b26629956a8fe184db67b97c459fe76d1fe56b7085b6f35195a33196a1ded1dc4a82733487af2204c6348f07d80f82786771e4ef236fa5b56fce8fabb64f9b2 SHA512 7f987de9aa54c46d32476d6548d239f823d413e5755fc499b6ac36a52da15792eb69ab6887c4fd3d4b228d2bfe37a7097978c851c44d1bd0e761eb24af9598e2
+EBUILD alt-ergo-2.3.0.ebuild 1206 BLAKE2B 4a87409f9bc9fa2fb3458e6be471488e40b0ee81bf96d8a28803ef5452d48d9d3e33a5be6f5e4ad9e009b4db414a8bee81a078206d9cf7deedc51f0795a765aa SHA512 1853517b8c206b339606f9b6ed787822291fe5240d59c9602d67ec606f7441bd1d1154fff96f17bf20887841d59ce131cf62188c18e0285a8ed8da52429c3b2a
MISC metadata.xml 670 BLAKE2B 5f03c359cb298cc9a0fea6ef3a5deb092e5ccca7acfb2b7a5630303659bfd853fe86277ebbfb1fb7b6677d45dde2d5c68d55fffa8d3d8187acac3765f52df7c9 SHA512 9e514e4da2b92aa1e8e8e084450f478b51947172b689664dfe6c0fe0eb139e278e13689c8ba53825cb3bc32140cfd4cd7a68fede0d013cd065d5339d34931e8d
diff --git a/sci-mathematics/alt-ergo/alt-ergo-2.3.0.ebuild b/sci-mathematics/alt-ergo/alt-ergo-2.3.0.ebuild
index 2f9029c56d08..668708afdc77 100644
--- a/sci-mathematics/alt-ergo/alt-ergo-2.3.0.ebuild
+++ b/sci-mathematics/alt-ergo/alt-ergo-2.3.0.ebuild
@@ -20,11 +20,18 @@ DEPEND=">=dev-lang/ocaml-4.09.0[ocamlopt?]
>=dev-ml/ocplib-simplex-0.4
>=dev-ml/menhir-20181006
dev-ml/seq
- dev-ml/dune"
+ dev-ml/dune
+ dev-ml/num"
RDEPEND="${DEPEND}"
DOCS=( CHANGES INSTALL.md README.md )
+QA_FLAGS_IGNORED=(
+ /usr/lib64/alt-ergo-parsers/AltErgoParsers.cmxs
+ /usr/lib64/alt-ergo-lib/AltErgoLib.cmxs
+ /usr/bin/alt-ergo
+)
+
src_prepare() {
default
find "${S}" -name \*.ml | xargs sed -i "s:Pervasives:Stdlib:g" || die
diff --git a/sci-mathematics/gimps/Manifest b/sci-mathematics/gimps/Manifest
index d373aeebfb47..0e7d3abacc4c 100644
--- a/sci-mathematics/gimps/Manifest
+++ b/sci-mathematics/gimps/Manifest
@@ -5,5 +5,5 @@ AUX gimps.service 283 BLAKE2B db6c0c777d514aa0216c1af087418ead25561ffa950752e237
AUX gimps.tmpfiles 38 BLAKE2B c306d739ed0a0cc8bb4c80c7051ad93326cf0054d3f7fd61c4ed8a7d518356d521f7d3c3202d0b8b69723b8e7178457a34c65e92732eb15e8e64c3dff468ae2a SHA512 61c5eda13289175cdf55704442ceab4d5391d24cfa49f04155799fc2798e5ad5f1e624802e1c04b99685b1560f9898d1b0fc0c15c82251d1a765dd5de93024d8
DIST p95v298b6.linux32.tar.gz 5696871 BLAKE2B e2c68c4dac1e4cfbc2e44542665326d33a7929585928ca720569b918f5286c97b93acc45c03d0514cadb29e87e5c6ca103e69953417df8405e36998c5768896b SHA512 6f82973237c59cd548fe7bfc08c51a62cc7ac4e98a8539e5dfbc23eec21fb6f46e1534dc834852557af61fa1a6fc9b634d9117d85fce37f8f6f9189fb724518b
DIST p95v298b6.linux64.tar.gz 7032597 BLAKE2B de4de01d68caba4530d5adca165bfaa28cdb7e276b44355b200245cac6bab80bc05885a994c06331c2f66bdcd236c8bdb6cc8206ca40fb583bce6dc98eced7b1 SHA512 cb0ea195f4167e22bfdeef02872205a40ccd4d110abc9c354a413284db9aef1dbf9888ecdc3f09262e0d1033c0e4bed1f23d4d966fb58c437673a81095252bd1
-EBUILD gimps-29.8.6.ebuild 1720 BLAKE2B 725dcd29f5e7bbc138659b9ff3a37abd60fd344518726a38756b1cc4c3e8eaccc08a7091b574a301106d7f5ae26abff79c4a3fdcdb29dd44df1d7a7f5798ce23 SHA512 9bc60af87a0e44f6532927bb1465f1b76e0d9c264c75cb9b9beafd33ca0de1655e187572a3e89dfae541c79f3621ab43678a45f2935d74e2897d9edc7c39f5d2
+EBUILD gimps-29.8.6-r1.ebuild 1746 BLAKE2B 54a0f315c0fedf1971ed17fcb0d2e2e184c05974f43556c2433763c113a7b382dfd9e828d6f51f338ded4bd4d273e55f76207f64b28049dfd50341a935d59d91 SHA512 3cf1f72eb72634e6e5274441dd624da5c3ea760fb69ff3a78146fdcc3d06a7ab801895f51fc49abf14dc9db239504dbf2da371bc88204d6a52731c84ac247dbd
MISC metadata.xml 529 BLAKE2B a6e3550d128d6c4801029726feb868aa1cd1017b8a2f6f7ebbb3743a7b2190d40db06d22eb4f8ce94e35ab5e6b1f213afdf179fe7777501ad87457be43d9af44 SHA512 a7fb9bd05f987e1d48a04b70e78cbb3906927197793870435fee8b68dd9da623a68fc30ca96d0173952414d9741674ba2cc2c3f821dfd7b302f91f09e887a362
diff --git a/sci-mathematics/gimps/gimps-29.8.6.ebuild b/sci-mathematics/gimps/gimps-29.8.6-r1.ebuild
index 262c362cf14f..5c5aef85e201 100644
--- a/sci-mathematics/gimps/gimps-29.8.6.ebuild
+++ b/sci-mathematics/gimps/gimps-29.8.6-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -20,6 +20,7 @@ SRC_URI="
SLOT="0"
LICENSE="GIMPS"
+RESTRICT="mirror bindist"
KEYWORDS="-* amd64 x86"
# Since there are no statically linked binaries for this version of mprime,
diff --git a/sci-mathematics/mathmod/Manifest b/sci-mathematics/mathmod/Manifest
index c5274f13aee9..d2185e0e4a2b 100644
--- a/sci-mathematics/mathmod/Manifest
+++ b/sci-mathematics/mathmod/Manifest
@@ -1,3 +1,3 @@
DIST mathmod-4.1.src.zip 974709 BLAKE2B f7fa5579b670b2512eab4fd7b706a0ca2282fb63356ea44ea2ddc6204b73ae2b7cd6f837d7622ebf0e51ba2b0127437b1836b59780df6c4b8e704fcb92e8680e SHA512 e7a170f5b57384cca4e755a0bb3691ec3fe29e9b22027534f1e84ed656905495c70eea8c69262f31a937ca508c34177d33adc23f5a8a3c91db1eceb2aa283a6d
-EBUILD mathmod-4.1-r1.ebuild 1054 BLAKE2B 0e8a65c75fefc383fae86cfc622793e5be72ff3be98d5c2f236fea422b3e69531e68afc7656805ed62b55cc185d2e8a3c375658fefad207bd588f46ae487d5e8 SHA512 4b49f4b769888e93d334f4a6e5fac8b9d4351f78bd2584dccbe6809932d70c56bc66efd3ad8e01b373be25771bf134f47124bbd4026b2a9b008ee18373de9d9c
+EBUILD mathmod-4.1-r1.ebuild 1062 BLAKE2B 387da9e68b15fb310ec33ad1f83e122ad1ff0fbef89826e7850fd7d86042560ad0edc7888e7e73c561491882d2fb4d5b1fd51b91d3f0cb1cb54d37d2773e6bcc SHA512 b25cfe1accfd7afe2015b23c0ccc875f821891d0b0a1dfa1d9b05842c83ec324e764f9516ed4e2c5c958ceaf55f2a7110ac6390295b49e10f6beb142850aa987
MISC metadata.xml 683 BLAKE2B 82c0500c4aa5fac79d7cef3b40c9116dd645c38908e579dceb9dade6a20a54f101e55885a033bc8ec8b3a5f9b51cc2c88f3f3fd6b635e98ca61df380db499a1e SHA512 e2eebe176c9128f359de88e7eb7ae2f151adac7bcf7bb2ebdd9f9a73eac08434d630e7445829426262ad882bde10f741252e4bf6829ffa00d06b21dc17d27140
diff --git a/sci-mathematics/mathmod/mathmod-4.1-r1.ebuild b/sci-mathematics/mathmod/mathmod-4.1-r1.ebuild
index bdfb57706c69..fcf1e631ed43 100644
--- a/sci-mathematics/mathmod/mathmod-4.1-r1.ebuild
+++ b/sci-mathematics/mathmod/mathmod-4.1-r1.ebuild
@@ -1,18 +1,24 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-inherit eutils gnome2-utils qmake-utils fdo-mime
+EAPI=7
+
+inherit desktop qmake-utils xdg-utils
DESCRIPTION="Plot parametric and implicit surfaces"
HOMEPAGE="https://www.facebook.com/pages/MathMod/529510253833102"
SRC_URI="mirror://sourceforge/${PN}/${P}.src.zip"
+
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-RDEPEND="dev-qt/qtwidgets:5 dev-qt/qtopengl:5"
+RDEPEND="
+ dev-qt/qtcore:5
+ dev-qt/qtgui:5
+ dev-qt/qtopengl:5
+ dev-qt/qtwidgets:5"
DEPEND="${RDEPEND}"
S="${WORKDIR}"/${PN}-branches-274-trunk
@@ -33,11 +39,11 @@ src_install() {
}
pkg_postinst() {
- gnome2_icon_cache_update
- fdo-mime_desktop_database_update
+ xdg_icon_cache_update
+ xdg_desktop_database_update
}
pkg_postrm() {
- gnome2_icon_cache_update
- fdo-mime_desktop_database_update
+ xdg_icon_cache_update
+ xdg_desktop_database_update
}
diff --git a/sci-mathematics/octave/Manifest b/sci-mathematics/octave/Manifest
index 63563bf553ac..0c203194367b 100644
--- a/sci-mathematics/octave/Manifest
+++ b/sci-mathematics/octave/Manifest
@@ -20,5 +20,5 @@ EBUILD octave-4.2.2.ebuild 5103 BLAKE2B 690f0a397a887a26d0ad7dc31af6893af0ccafed
EBUILD octave-4.4.0.ebuild 5082 BLAKE2B 8736fa239d93b6847d413e50cf75427bf16407814d5d32f55f2d8688b57fbeacb471afd2a86ec8c1f6a1c1da11882a40dd221e5eea9fdd0ad59e224c0f1e5d65 SHA512 b71030ab908c404a3672d1df9f85e2cf3aa99f4e6e968ae90a95af228912e4615e869d58efaa018a7cb1300d4630111af82bc306b3d1e56340df5dbd1065bd32
EBUILD octave-4.4.1.ebuild 5180 BLAKE2B 495f7aa6fc5508fbe2285e5fbc8eb7a4055d84e538384487c3f535f9d5cb90bb3c0d896455d05a02878d786a0a338373380f8e955415673a625db17cc80a14fe SHA512 b26dd91d325a55a94da6eb4bba15f279f3d8c80dcecc19c53ff3d8c43c664aea45769b0f3310a38addab326bf6bc59aa6b88b2b07981d731803d82865989250d
EBUILD octave-5.1.0.ebuild 5076 BLAKE2B 6f843fc6ff0157c6e4f80aaa2f2cc056c4215483e0b62b809821e8f81234caf8be57bb9232fd305fb2bf8d4266de452b7efa20c208a23f4aa7ca4e038785adb3 SHA512 41f83b3a3431a103b10a654573a8d7cb5eb1f45b79125e15818d8f2850faccd5266ee24ee102e4bed0452ba17a3d8999ca755830fea353ada4dd973282a5b0d1
-EBUILD octave-5.2.0.ebuild 5462 BLAKE2B 9b76e5654e712b254cf2151bd3cad205a63bb064ce0b58d717c73097a8f7ffa2ed1e2abfafd1d30f6e6e7a2913a0159b8c27f069dc6640471302c34d5d77b615 SHA512 77d4843fb0499f145a3ac77f166c8f5eb92f236acbd48154c70c94e02a2bcb74175a0e28384686e7a4ab42210892a47d3578d26b25947d0a0f41b611da0f132a
+EBUILD octave-5.2.0.ebuild 5461 BLAKE2B 6e31e77cd0ed5e8c6dd53fc8959cbfd4f89695df7545e40c3038ff7172108c2d9669d79f3af0c6e638b4f4a68703dc7faa8a77ca8f6671870c1cb3b755088450 SHA512 4b9628bdf4d55a37ed29f7b1dbde04b302f3ddccba10f3df424a1419d59d01ca16c39ef421b341a3e0434c19bba8ec5cafb8e5e191b2c9dd8c213aecffe39ac0
MISC metadata.xml 1137 BLAKE2B 69a3d32e58fcf2f855b54664e1fb4e0f2eec69bd8522218957320a0d0f8bf67fb8d5e28f7f108d3baf7992454adef3a416d4bdae9d7b4fd2bfe77225de17a69e SHA512 7351fa4b9a696406543cda7246378e4b4df4dad3033f9a87e4c5036663fc32965c7db45d8ff32959904a9bf71cff88484b542bc3e20ea0ee946a0025c091a345
diff --git a/sci-mathematics/octave/octave-5.2.0.ebuild b/sci-mathematics/octave/octave-5.2.0.ebuild
index 5d9b11ef5c5e..08552a338be7 100644
--- a/sci-mathematics/octave/octave-5.2.0.ebuild
+++ b/sci-mathematics/octave/octave-5.2.0.ebuild
@@ -14,7 +14,7 @@ SLOT="0/${PV}"
IUSE="curl doc fftw +glpk gnuplot gui hdf5 java libressl opengl
portaudio postscript +qhull +qrupdate readline sndfile +sparse
ssl static-libs X zlib"
-KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
app-arch/bzip2
diff --git a/sci-mathematics/psmt2-frontend/Manifest b/sci-mathematics/psmt2-frontend/Manifest
index 1c63be52d587..3aac5e4f68bb 100644
--- a/sci-mathematics/psmt2-frontend/Manifest
+++ b/sci-mathematics/psmt2-frontend/Manifest
@@ -1,4 +1,4 @@
AUX psmt2-frontend-0.2-gentoo.patch 607 BLAKE2B 4d3a967d9c694e74b1e33426d73f41e97be37510241291339e4d7c4e677ef247cc9dd28728df4fcdb6a0819aa8d1ccb6233d65cb206cbf78dcf9004af7744a7b SHA512 6ec9c1c89ceb023b57820f083722b4c4a693a27c38fcc63a9bf6403853c716a398f055a8db579e683a03f2ca8ccfcd9235796ce1f44867d47805279f6a0a8700
DIST psmt2-frontend-0.2.tar.gz 26976 BLAKE2B 2b45ceb8d824f5b11455ad0026064b6329b6c6e6173c091b36dc42e8c1dd36924d12d9296db3dcfe748a84fdc37a1a530f3ef485bec904c19a0e6aa8034149f9 SHA512 c29802f4265a1cbdb05ee9154ce2c156136af258bc7283dd0fb1d1b2ce162b671553cab96484036d898e3ff7c26ab133f5c2e1ca88e9e48660b2faa139fd1f41
-EBUILD psmt2-frontend-0.2.ebuild 716 BLAKE2B 3d44765040405bf5beb779dd7f1fb388c0dfaba41aa14d84a144482f7acd5c354e87845b24fed33e145981850124a1ec73e4914ec091ce9eb93b0f56631cb3fa SHA512 678f6e15cff8e3d1cec09affed6e70e6ad596f9936fdf8f87ac69c08eacda841a0e64b92a6bd3420683fc5a661969569b139ff0a996cec65f90680ba88b586a9
+EBUILD psmt2-frontend-0.2.ebuild 949 BLAKE2B c86ff25357b7d930a560559921f063bbd9fdfbe055eb2e06413e3619ec1834c24052718b30e022be46761846c57176e81fb5fa0374bb98b2c2be41b31c094a3f SHA512 db228543428bb17b0b7bb313deadebc6b01edf034bd48879aeed33fdb26a90f5cd51e3f95884dfff5bcce77a602ac64d95af7a4390350e96d7a77d6d89801feb
MISC metadata.xml 247 BLAKE2B ca08677c4c0af66af431abe578122a2ea0278f7ffabab245eec806167a6226c65f97e9826d64fc4b82eb14b6200cd1e3a31a5b4999e18aac41a4f9af43d708d6 SHA512 fff6c25e644477aaa35b838e10c44ca8eae9824ef8f19795e31201db40c10068f0216dec38deb0ba80782155b43fd1d72fb888cb825eaabacc3bd1ec0d18f3ca
diff --git a/sci-mathematics/psmt2-frontend/psmt2-frontend-0.2.ebuild b/sci-mathematics/psmt2-frontend/psmt2-frontend-0.2.ebuild
index 5f6f9e6f4f39..09760d868d06 100644
--- a/sci-mathematics/psmt2-frontend/psmt2-frontend-0.2.ebuild
+++ b/sci-mathematics/psmt2-frontend/psmt2-frontend-0.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,3 +32,12 @@ src_compile() {
emake depend
default
}
+
+src_install() {
+ default
+ QA_FLAGS_IGNORED=(
+ /usr/$(get_libdir)/ocaml/psmt2-frontend/psmt2Frontend.o
+ /usr/$(get_libdir)/ocaml/psmt2-frontend/psmt2Frontend.cmxs
+ /usr/$(get_libdir)/ocaml/psmt2-frontend/psmt2Frontend.a
+ )
+}
diff --git a/sci-mathematics/pymc3/Manifest b/sci-mathematics/pymc3/Manifest
index 516fc1e3ee69..b8c95da67934 100644
--- a/sci-mathematics/pymc3/Manifest
+++ b/sci-mathematics/pymc3/Manifest
@@ -1,3 +1,3 @@
DIST pymc3-3.1.tar.gz 34553828 BLAKE2B 73c4d50f7d656322fa1a7384aefa1f46caacccc8055138fefc27a82d765866efb9d4853a842a2df312058c558edd66b37a40295904c86f023f8fec5503877206 SHA512 30799d9c1b670adbcf5cc1463029d71a87c7b917e83b1f6cb453d75553616da7173421e7ae6e31b332c85f8170daea735344ff83ba6605cf3b15cf79c5c4fb97
-EBUILD pymc3-3.1.ebuild 1531 BLAKE2B 8e497bc9fa347d879cd356bad2100fdb60c91c35838d703010f2ddd990bd7a0c773b143fafb3eef1f29b33bc682f1141bcf545c51a4ab57a42a63405d439eaed SHA512 d9f0c88fb2708626e2778c163bf0b31031e219c664356c11478ede36923e8c288af260167fd61711282fe40a70ffa588a84b63002b8207bc0796d5063a741a62
+EBUILD pymc3-3.1-r1.ebuild 1433 BLAKE2B efcce10b67f51d4379a3e15c458513b5c058371c148f4f879a5b2d45c3c6d7a87f5228da33ed5526bc65c270e02f161341ff1a39667a5f07bddf730c691145a7 SHA512 a4dd49af5c79fd3521e24f2750187693f1256d97267eb06803ecdcc83a0ab39eb027460a574fff959cec88e622dba3f682105f5555196d2279aa128fec9571ca
MISC metadata.xml 740 BLAKE2B 2c56161497137f40e0e25e85299af90c361ddbcaccb4436747ba111e725c9a881fdf88944dd0208909275bf4013b9e1d5983b590ad7f46589f584549288aa02c SHA512 c75ed4b57479fef93c4b667792cb284212f859532697c4d4876e2dc23ab13d2c470143d3236de03e741a0797049a12d3a7e2f0d2ae4f07b2cfb0b7943c78526d
diff --git a/sci-mathematics/pymc3/pymc3-3.1.ebuild b/sci-mathematics/pymc3/pymc3-3.1-r1.ebuild
index 3c95b008123c..b631808b810e 100644
--- a/sci-mathematics/pymc3/pymc3-3.1.ebuild
+++ b/sci-mathematics/pymc3/pymc3-3.1-r1.ebuild
@@ -22,7 +22,6 @@ IUSE="test"
RESTRICT="!test? ( test )"
RDEPEND="
- <=dev-python/commonmark-0.5.4[${PYTHON_USEDEP}]
>=dev-python/joblib-0.9[${PYTHON_USEDEP}]
>=dev-python/numpy-1.11[${PYTHON_USEDEP},lapack]
>=dev-python/matplotlib-1.5[${PYTHON_USEDEP}]
@@ -30,7 +29,6 @@ RDEPEND="
dev-python/numpydoc[${PYTHON_USEDEP}]
>=dev-python/pandas-0.18[${PYTHON_USEDEP}]
>=dev-python/patsy-0.4[${PYTHON_USEDEP}]
- >=dev-python/recommonmark-0.4[${PYTHON_USEDEP}]
dev-python/sphinx[${PYTHON_USEDEP}]
>=dev-python/theano-0.9[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.8.4[${PYTHON_USEDEP}]
diff --git a/sci-mathematics/rkward/Manifest b/sci-mathematics/rkward/Manifest
index 2430d82a2511..f294d909e79c 100644
--- a/sci-mathematics/rkward/Manifest
+++ b/sci-mathematics/rkward/Manifest
@@ -1,3 +1,3 @@
-DIST rkward-0.7.1.tar.gz 4605097 BLAKE2B d2e0af7480965f139b1c3a36da9c9b0c005aa51f94df0a4622718b84bc8de9799e2d861972cd0bc0b4cc685c39cde9f0c2df90166fd8513169806ba6bab5cf95 SHA512 acb4eb8884afe44d7522cbf69980614d389318accaf085986e68283447626a6b890e09a1fd48c55cebb194fae40d9fc14af01e36dfed00a0b45733e61ac9e7b0
-EBUILD rkward-0.7.1.ebuild 1087 BLAKE2B eaaf8f0588177e88e7b23468e3eefe4c5dad2d982e5ea51980e6e5c1d87e52cc6ac9758003f0d0d17815839a7af83b24a24204d8bf61ecce451a2447b9e371eb SHA512 cf4842c24ca8fcbb9efcd5f8f596931d3df6bcc9f9bdb3d166fbbf4c1e3bce747b98cfbc9e08e4749ab6a2eec07cc3ec8e273125f292984ff57410d1dea02862
+DIST rkward-0.7.1b.tar.gz 4618168 BLAKE2B cccd0409d6609aee500d4a96bbe9d94fe7c3b8c7ee77d0b80e0b4e62445bf9eb46f9a1c2ff82a11c304d3c58c8ef32f33b2aaf2a96faa9e69adb10f1fb6a5746 SHA512 e2fef6db00153a67e03ef6a4e8152eceee45738394758042df1248053c1473a362cf70615bd4d8451b6594a252e16875d9248c1a358f33a8f1917503e22b4cf8
+EBUILD rkward-0.7.1b.ebuild 1085 BLAKE2B cf73b465ea4dd14aff0752383756dce6f10c2c410f6fbe976fb13d9a1aca2ff9e188f244f882215884d2fc508823d2b7c91c392c9f2f4941dbd4c3e51557be8e SHA512 e4b7b317499b43ef31d7f6e3148f7c6c9fdcf50d525826a2ec2bb5d6ab1fcc5ae781749f5281834ee822f40c4588aa9eb5418c1a25f65c694dc46c944f9f6b31
MISC metadata.xml 592 BLAKE2B 887f22ad10d784dd1a12f50ab14ae07e9da5f90828b78027c08c864641e334cd1343bd4bbd197ccec086fe9e7d1e95602f8f78cc3f1316701900b73e266d763d SHA512 81c026c96614186bc6b31f9737b91692df82523d2179d467aeb663f10b7ce079a4b52354d8f744dedbe5bf5cf1939921a26f24f8deec9a170ac435da1f9863f6
diff --git a/sci-mathematics/rkward/rkward-0.7.1.ebuild b/sci-mathematics/rkward/rkward-0.7.1b.ebuild
index f94c4af33685..d9b8f8cc9ce9 100644
--- a/sci-mathematics/rkward/rkward-0.7.1.ebuild
+++ b/sci-mathematics/rkward/rkward-0.7.1b.ebuild
@@ -8,7 +8,7 @@ inherit ecm kde.org
DESCRIPTION="IDE for the R-project"
HOMEPAGE="https://rkward.kde.org/"
-SRC_URI="mirror://kde/stable/${PN}/${PV/b}/src/${P}.tar.gz"
+SRC_URI="mirror://kde/stable/${PN}/${PV}/src/${P}.tar.gz"
LICENSE="GPL-2+ LGPL-2"
SLOT="5"
diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index e74624932965..9e8a45e50785 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,52 +1,29 @@
AUX rsession.conf 1145 BLAKE2B 81e0ba1c273cbebe1fcd95917cbfd9269525e4994f594734207972948ffbda5f500483ea21678dd15f28aed25ca060698f710fc3586522043347e55d3f4890a1 SHA512 90395faac5aa80ce52ae56da3565512b8a880a14ab2acf9a24c7a56c9d03f1e3d5f63ebaca66efa68f5c5c9c831235846df22ca37f20ba071437a2a963b808cf
-AUX rstudio-0.98.490-linker_flags.patch 806 BLAKE2B dc32a4a3bbe7ed2467c187aab7a1cfa0dae3862db8b091edff69608163181f4d073d94a58ce017b94b5d4701783eb41561de5e1b4a73a49ea349129f4a8650d1 SHA512 2049077768ef72faf502387b5eeef80948d0ec748bc52df7bff6e507dd92a8c52b3a7f7f82eda526ea1289f16720ae51fd40c059bd2d04f5eacd51911b995f06
-AUX rstudio-0.99.473-qtsingleapplication.patch 1889 BLAKE2B 1346ed138abd08318f23cbe4b34a0d2ee4ac0cf83206eba04c238c08c659859c11e207e3e6d03ad23e5baf6353a5f8ad49fbdffcea31104dc810fbb05f4ec9c3 SHA512 07af71ac080c0a2d4c2c62ec8f0ac451e6100a94e5360fafd274c62e2205d60d0c4b7fe18ed4536e515fa4a51a4ab819e47c529ce4fcbf93532dbb57e123fb37
-AUX rstudio-0.99.879-prefs.patch 1859 BLAKE2B f324ab7b87e7cef32ac8b2718059200e4040d82258ba6d47bf41527ba413627b5a0971924ce3e1bfa1337d206838cb9f1ade11a1fe35786fe2371b0cb86a4c11 SHA512 987d46d7dd8955ae55f29aa2ca51241697405d8219b719342a5e8b6621dcec8bffa5b41d09a82e03d65c6b9797fb6aea8791ea161f4406600a5d5bd20aaf00f8
-AUX rstudio-1.0.44-paths.patch 6722 BLAKE2B 46351eb6eda15f74b03f1c5beb0b22bb835f4312af1889997e042657383a0130986bf4ecbc45dac98aafed7c317048e8bb380287a79be696c5c0a403e5633857 SHA512 6191520733f33466cf45bcc102a386763acc37a0cc1c58718cb59f3e3b5549afe5a051039f50aa390d773433d992cdff11bdf27c7e2960eb6177cd99c3169828
AUX rstudio-1.0.44-systemd.patch 1060 BLAKE2B c5417748653b60c85cacfaab08f2baf6936c3c2d76fe0c23702fe006c4f13de9d17a3556c05c0f47be41c6f4629d92da265861b1c689415bbdd59a515d1848af SHA512 3559fc0cb229b50fbfd4361e5be982396d563e41475878f15f870609caa9f85bd50b32f90b8f8d9c432287cb7286920dca21279bc5bfb33f1fd95a0ce68a2c4e
-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 18663 BLAKE2B b6431c931c97bdad30756e62510ad839c86f77e2474faace7202ef596fe6d2e06659fdd82d78135456a7ed9b343df0a309432438dcd7a87b5cde2e0b690e3be3 SHA512 2c86971f29059c22d97680cd8ccbcdab19873f28929b71079f1d3cc004ea3625ebc4644f49c0ac9fbe4726b8d60c76cbbd882e8712e76cd0c939a2a31fe6f945
-AUX rstudio-1.1.463-boost-1.69.0_p2.patch 8514 BLAKE2B efa138cc72890872670da80e688f4171f8ad3001eb3a1f8d549e6841857f97cc7ef54c02f39db9014a73dfae03f206ac6dc8c274c02c8c644f4738561f3c841c SHA512 6cbfefe675271fe131858f0753e93008a72019d24888c517b09cf37c0d944d71f5f63575eabb0d0f524419052a77f166f1b039f43fae51cd40bb82ac225716f2
-AUX rstudio-1.1.463-boost-1.69.0_p3.patch 7744 BLAKE2B dd8c4f40731e5cde1d277a29f7db9068db1e5da2e329558911afc5bffa8ee80e727e674383cc3c16e7b653e62895f06782aa9505ff102086e9e3bfdb822d9a5f SHA512 ef41803eea2efd4f5e309ede41c54e77115a358065fd3d4c3a2178e6bbaedc08a619517b28672d6003cc1c9062526e3f881645dd99cba57d1de1d13c643cd391
-AUX rstudio-1.1.463-boost-1.70.0.patch 1765 BLAKE2B 43520b4ef0c20ce33cb336d5b7fd0a2a30df74455ed1ed43dcb6d556970d08f61780c8a4ba341c5f5d4b3ae9023996f5ea76a0dad8c63fe74b535632650825f8 SHA512 7bfd9235ce0e3f45fdd4f4440c56a5172f0162fb65d4a784b792463defa8ec3013be92b16bff295e87ae01b3288f127386e0c07f0c8417fcc1f124db052eb9bf
-AUX rstudio-1.1.463-fix-ptr-int-compare.patch 595 BLAKE2B 10b7320990869c07c02e8a8cd06d41f67d0ddcbb7351fbbd2b9044144733b0b68225bc53c2aa93a98ea6715031d31346209700fbcbcb4c48809d9e3537cce435 SHA512 27fc52d4ff2a96212863eefabf3d69f4d18db259da4e366a0020c2deb4126d03208c9bf3c4877f75ccadaf5cc59da070a07380968d44942622525b1f33db90e3
AUX rstudio-1.2.1335-boost-1.70.0_p1.patch 1771 BLAKE2B eaa29ff256b8ee79c0384075745c53999d2d4ace494c0403cfa805868638921b6b0aa48631c8399bd8f21a4ee5734c6e0f46d2abf5f5111466613fbf7eca73bc SHA512 01a105c269147e256a3a0d2f803809d215c492c22626bf8b7bd5d9b6465db584b8aaa48299a6cc4f7081dd537ffcdedae1e2c328fe9bae0e1dca844f13402586
AUX rstudio-1.2.1335-boost-1.70.0_p2.patch 1081 BLAKE2B 19e78cfa2620335cdc2f058b84eba48f693d2cd3268813fb226641727c0f622bbe452d29bdd2be85518aaf4268306cd5e985ec5778e08f21bd802bfd5ef2eb2e SHA512 20c57a4eec8e8b333c718578caad1aca525df94090c7528f996077aab4a1a59d77a03e01d8ed2d3a77d444bebcd9744815fc168d2c3263b2f0b7646c5ebc37c0
-AUX rstudio-1.2.1335-boost-1.72-filesystem.patch 1057 BLAKE2B d375ad438e66f36d5cd0cb70572d164f54407acd6823f8c76571b40cce313a7f79afa63e44e92efc9a764bd660ace471f8332a9032c9f7b14fbd2e8b4dd325a9 SHA512 83b70516cc16564c175a6ceb810b27b2e89cea37c6f1f789871d2d115ce1705246edab06395bf6fce7951a5593017fae015571304f6ef36deb9efc13f1c388a7
AUX rstudio-1.2.1335-core.patch 6336 BLAKE2B 00abd96a9d653fc6c557e9e3bd82227ead2edef5a49ae67ee0ee4ec97b5a80665c999f478516710c437a0148b9e3b372164aa5e4c50813db41de0eb667bdbd41 SHA512 7cda17801efd5afe91d9064c7c24bd285ee1c2bc2df3f2631fe68261194394adb217345be529b5a6880a93a99dd6f4f32a92d449ace30c31f6d85cbf79f039fa
-AUX rstudio-1.2.1335-fix-ptr-int-compare.patch 595 BLAKE2B 8db7be4c0be67670d60a8f096faa58b13a6dc87194d0997cf97768d8fd67e2c74b84c4de2a8f4502bbd9cf262293b8fe18f4d05428394dcc70ebc8962a969923 SHA512 2f083f036f3594af206fd71db5b761ae6a536e99e4b51264234a7d8169db252b0494da19d5e9d319817a84f6002f64ccb388bc6e0a42bf439c1365618da5626f
AUX rstudio-1.2.1335-linker_flags.patch 505 BLAKE2B ac0ebca22f6dfcb799dd151e3c915c387dade30f86a9d335513d75c7c726c362255c745e91949ef3c1f58695d7a76a53550837c9d550113ba81d3d2d36507459 SHA512 221471a6ad720517a0b62563779ee11190f14b2f2f6d39e9e1c0acb32a03e41b9db5bd639c5336a26936d8f71ab5d88274471b00d224c6e31f2662680d6fd71c
-AUX rstudio-1.2.1335-pandoc.patch 1392 BLAKE2B 55829768d2c05c5bb3ee13da383a5f9f084c788860acf2c7be29b526aaf2ae0d2c3872490867b20efdc2b132f3672dcc218f76705bbe7091e2cbec2f0460fb44 SHA512 6da7b7aee8d90bce1ddba8818a0d4a57d65d656dca8e487c81e27e03ac7aa973066d96a4c4bf5a65bfb73d5746af71b072f8a3a86daaef62c02f367bc781841c
-AUX rstudio-1.2.1335-paths.patch 6105 BLAKE2B 249118b4ecdaa00ad7192079f3d4cc38b623fcf82e4c1df688abefcc5d0cb17561fd5f873ef57a7338fda9b792224b7a166186ad13c84e18d975a4a21d7696a5 SHA512 7af93bc2e375a8070d22e3e923fd43135e5dc8d1875a6a206b14b92a07a20ed541cc6258cb92ce18e562d7247abb60e6e7e9d3fa680b6b9e8b9c34e8d93e4b1d
-AUX rstudio-1.2.1335-prefs.patch 2221 BLAKE2B 659738473f343ed1632221d33770d6caf59c1dc2cce6ff8e15e6742e3603edabd1ebb7f2e809837855a4dbd6792ef41668adb423a2a0a7ddbe378306fadaee20 SHA512 ba2b8f9186c97f17d265e475ee7e1444a4b9796675da2ac0148bef791aca4dda9a6b597c83c580837bbb55c53ea3f61871cba6b5bc60395c6a59e2778da3432f
AUX rstudio-1.2.1335-qtsingleapplication.patch 2080 BLAKE2B 3e2c1b5df1c030a0d3f9adb01ad469a7e4032248eca156644aa74fdbf1a4584fd92185c9f3e38cb8ee8afdfd556f40642995702719b4d69fe9342f9e4de85dda SHA512 6b03194d47c7f7a39b13ccf93d02bb154e85b5d46777fbf5306e94da13f22fc83bf91bd923a58dfc9bceda517cda81673deb0f0a7b087d501b82a961174bc9cc
AUX rstudio-1.2.5033-pandoc.patch 1442 BLAKE2B 28a1070057624fb70a2df6de0312dfa827a075ae481f6433733cdc6136a429fe67c72262d3106c6b00f7411f93d3e33ca69f232cc87aa9d8e50e11cad89d2dd6 SHA512 cdbb97f0705f6b56ce8e285d066c57a9f73ce87ef58d8101362a508cb1cc52a32418a742e84a9a9d6476b253984abe0759b45e824d360d8b550e53a98d2d05ca
AUX rstudio-1.2.5033-paths.patch 6055 BLAKE2B 1c389cbd2980031080955c104e614d2bbcd0d747fd7d925a9650685bf30ddb84c34b66a4a6bcb58a1b18167e51804df9c22734460255eda866365231cda3e9f9 SHA512 ba213cf13ae15df043215e6b87bf554c9daba4124a1a83ecb2e5ccc8f26fd6f1467798901cc24451f04f4d25482da401cc9cdd5071a4c6ac28d9af37c45f51e5
AUX rstudio-1.2.5033-prefs.patch 3684 BLAKE2B dfa5f7289a7e752704b6481dd6e02f8e88a91aaa36b25c91e8154f17bf3fbfcb2b674fcc790a82ae14deb0718b1d001f4931de6d6ccb99d1ed4dc9c8e71d6149 SHA512 86436aec19da35d99ec64ad1d4c243efad85a277ee72c2eaf94627c49389ba8d4bc626177a9d599bb95d00bc3e66210472e11a5ff38ed74a7a353a719f64fe4d
+AUX rstudio-1.2.5042-R-4.0.0.patch 3516 BLAKE2B ee54ab84f373c2d89c9bac238cbb500e10e542953522dede105885675e7cae319a5cd99ebd9cbceab903532925b950e827ab218cae8ce91ca58b0221ec223659 SHA512 872335efd1fbd8ec01c812ce652285220dda0ab9b53a0a044758ea7d7798a37ab3969e5c82e909139591f18716b0fd50538ec3ae264946ecd037b6bb1f84af38
AUX rstudio-1.2.5042-boost-1.73.0.patch 728 BLAKE2B 675e5ff75ce5c3242bff5d92b32ca6391e8ceb68c504c2f161f2f30c083ae842e5e9a9c519e848595704bb6d639c5a8dc13a296dcfa445db19295f8ee78168e0 SHA512 214751fff5b027f407b093f397e70e701ed9016451a3972b240dcd4999d9b27a1309b47fb22a9f4f3944c47dc6de6bd8f1165a70a7046b5133bd88923d1b46a6
+AUX rstudio-1.3.959-R-4.0.0.patch 3514 BLAKE2B 9cdadbf402f4f90f9b6e43155ec22d0bf22bcd33c817b7ce67646895b3d5672e5fe412e2ea891d6997ad4eb76dc4c514cb5f8ab06467e4c79c52875476bac7d1 SHA512 59b80b284bac4f1435a160c07a7959a4db4c7c3474d13c1c0e90f5bee34b017fd507618914fd249c14fef41535c06e78dfed22860c104c679e95a4782b1bfac3
+AUX rstudio-1.3.959-core.patch 7302 BLAKE2B eceff2aa67fc1a1cb36433bfa0956a4a45da3a017f80987e14893018737b3fc40cf1bbf9641e900311db3f5182828b11452c960b40c4e20ed83e5c3692e458bd SHA512 cf4e0682e3961c1208f14055bc604c2b8b8cc6db955216858ef4d95ca91154ab4d1eef58fcb5cdea84b2b755c98cd837b9028dad1520dd9dba222a45074a68f8
+AUX rstudio-1.3.959-pandoc-mathjax.patch 1997 BLAKE2B 71d40c2299b0598f9687175fe464d334e821762972dc0c4027f71c124eef2fd6795030c4426cec56c6b4fe81b8b72598f97214bab1d2b2b2a4c0c551cc1421a7 SHA512 6a5a76898500d3a8a20636a3854d459e5b8d806f68b0a4a08fcf3dae98feeebe751c14a7e4f8275c02ad47de9795168d90505d4dada19ccbdfbef0e07229cb66
+AUX rstudio-1.3.959-paths.patch 6142 BLAKE2B ed7ea6025e919e24228ea55679b198496446bc711e0efd355e1bc4ed4822078b8a486fb8390aaf6cf5852447fc9405ca68099e4a566b24521d341744c7e719a7 SHA512 9ee6c13619d6dac9f7af85557be1c4430d801424c3b29cbc73b657686d2cba49476083ae2bf87f7cef0039672116d3385fb51a03e803d9ae02e4a721403e614a
+AUX rstudio-1.3.959-prefs.patch 3132 BLAKE2B b2d815c8c08b1f9fde82e41fe1c865d0d70c9ecec729e7c62bf858cc48ab00afbc99c59086b0c2c7ab1e0a0a956fa6f448dd407750d4e92101e6609ec2e59ee9 SHA512 0e9541dd7fba278339b0ed409be9997c86ef3ed536de791cce98f9b718476e9144c53be1572fd3f4d2396ddede05df625b4d584aa7e83add7e9ddc41989c9fcd
+AUX rstudio-1.3.959-qtsingleapplication.patch 2149 BLAKE2B 5d7170aeb02fff87bfde9ad55c004a3690c6f0d2ea73602e22c17a79efa81a207ed83d23595e4e071375fb6df60d57c9f17380fe3726f57b3e126c0448560fe8 SHA512 b98761454a0afb64806409f1e330557379cce7f23aaafd3bdfe913f6d41b56738bcc746e99cf5031c8559fac5368dcd299bcbe31b7f40e3a3a7a8f92217ace05
AUX rstudio-server.conf 1337 BLAKE2B a9a85c76a1c7c5f32f55606c6e3c9b72662dbd25e4b005f9702ed301afc21425906faf06fca91c18328524c53437aee7c9c4aee26cf293cdc72375e91ec7f701 SHA512 f166f1aa4bd370fcfcb44c5694d4e6af8bc64c5f43671e0c1def10c555d248bebf54199097f37d628a083c65913f522b7b44c3bd6a1227c011cf25eed1dba4a6
AUX rstudio-server.initd 377 BLAKE2B 4f49b9ae2a81cd60565f79f121d60f5531746febd1f6f68cc93863985bd9af28d4ef04f647bd1b492ca69273724c282bcaedcfb5d08b8f2ac237ddb6f5baa438 SHA512 828a485338088d129c57debec6557ad35db5b042c61489ae4341717ce2218bec59a873541c270f964bb9c708b75896f1a3e2e64a4245a1713979d3bd42c9d5c8
AUX rstudio-server.service.in 161 BLAKE2B 0be9cb83304063c9123c6fa13b7751b2f848adde282fc586acccfa4110f902e4de9962211ca0c871f66f3563319fe195c9f230daa4d4e429357ff74701e4d2d7 SHA512 bcf1f30e460dd5f0562b20489ca5544c6bcfbfb0ee1c636c4365df433e97e02e9e3b233e4159a0c71ad6d319f34f93c22b8fbf6b36463e29f22df2acd71da173
-DIST chromedriver-linux 19303552 BLAKE2B 610396fd74f2adc4c249ca971a53a6dd4ab06145d0b37d59adf66180dfada52192b20203bf3d992c270bd4f787df5c85511ca325aed06cbd9318add3eccfde30 SHA512 18774ede961dec222058dd0e3f128d63732cd444ee310136b44d5bf508a4f2f2c164a2c8d195d80bce8b5fb6303559e167f82f384e4a58e30f48b151a4206ee8
DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18488f54c9a09a2b95fde19b796e4473e5846402a46dd24b71c6e4167512539aaa32ab6d99713d500a80aaf46796 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9
-DIST gin-1.5.zip 1055663 BLAKE2B 11b86245d54967f0c76f22f7460fb752c410db3c59a019bb538a48fd0de7e87552f2f5bb9ce604e6ed508136a6a2b0814f061161579429daae8ca55b1a448114 SHA512 3f6649565f9600daaca6ddf3fb431925b5a1ce1ada38e6389de64cef617abba9d3f49c555d0a20053fb06f17ccbe4e1141b39966fbe4b2975d7b120377504897
-DIST gin-2.1.2.zip 1341053 BLAKE2B 515338ba50ba2183c101b42183e42ebf15613aae8751a0dcedb4b047de4ca8fab85eb240f5f0c92955441dbb87e80b3edbdae8d83f1e74f74c7de067d18cf108 SHA512 03407b6318ffb0dd504ce520649ed90e845f13fbdbd0bfb4d7e3b127842f1735093e39674077c3a04a11d434aefdc3a734652c3f85e8ab00ff37ae760ccb8dbb
-DIST gwt-2.7.0.zip 108818328 BLAKE2B 9af969f3f2577be041fcfb58f228fab4b5479fa0da5ff054ab0a59cad751590a1b4ae8d7fabc8a50e3b0e5d7eb9b2896c485d929421f75e6a2f6513480438a31 SHA512 a1eed5cc25c888cf81d4f22b1f9494d5d8567b911f7aeb1d164a6359120543668280afe1a3ffc9ed87b139c7db67fbcaaabde2066e3279909d7cd6fc22eaf499
-DIST gwt-2.8.1.zip 95650299 BLAKE2B 3853d50d1346e313903b6f0c4b8405ce9e896e51652483e5c7e9d711daa213e1341c71765b4a3fb061b58f90d49420245963a0480db8b71fe7aed6cd43782c14 SHA512 feeb00cb0413c2703dfd6931f57ba669813bd65f814715f2c04dd6dc69e885a8048337272333d7504c48e9fa52cdab699f854ee13211228ab142a1f458ee33ae
-DIST packrat-0.98.1000.tar.gz 97677 BLAKE2B 282fe33dc5ba366ceea05a222ae2d018bc3ad8f35fad73c585a3d4901c3287e6902277a9c7ca087854f3944bd85ff1b1d1f02869ece686b10f946e2f1cb1296c SHA512 2290c768ecf27a037e73c3f8336b9fd71c68ff19d071b4a8fbc469550d29007cacacdb75f854f73b5db2139a5104f129b85a3612e2ee47bd6118ee13f7d103a6
-DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852
-DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
-DIST rstudio-1.1.463.tar.gz 20203779 BLAKE2B 97f879539cbb7051af362a8469795a47feb42d18ff46dbbdffe36e0685d1cd5704848b3bf5a5611d482a09567722e35288527302cd521b18e2a48b347c919e17 SHA512 987347563a9726363c28d866e1372eae8eb19a5cbd0e33c7ee0e0c8f90471c4b69de0f559c00410523841b6c090b584652e01496f5db33c015a4554d2f4e179b
-DIST rstudio-1.2.1335.tar.gz 20440199 BLAKE2B cdd54a7df5a234bcc6d440f4ba5b45e58ea469f8dac5a17d9088f9d65035495c86b5a308cde28a224648f96a74038299863291f3c516a1d567762ecc5bfb079c SHA512 90657effc55264bf3efa1a8a5d2bbe94a37727f0450202ade99b9fbb71ea75b6dd9fa798d17cd4d1a1a97a16f186de8004d1888b6ea43f36d5252508520d3cde
DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
-DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
-DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
-DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c
-EBUILD rstudio-1.1.463-r1.ebuild 8689 BLAKE2B ab91995b112b4d3e888c688b72109ed47468c8b72e13aa3066ecb51c213a46471f42f5bb517e8e2a82a623771eeebf917c02d85cd4322dbb1992687fd93d6c86 SHA512 0bffca8ab03f91e4aa2ee24df21b9a102260eb587d1127f885d591221171dd691c347fb87a5e11a5e191c9a363daf13210310acafbb47405951c2bc2c38c18d0
-EBUILD rstudio-1.2.1335.ebuild 8688 BLAKE2B b02dac6ce848799534e95fa016d481526bf09525c84834f604dc6cbfe625e2b4d278fc4554119be6edfd27ad987c4cb9cfa48f56f0c5d165450ea8bfa2a7f276 SHA512 fd846f875b2a9c3e9e992371b8cd11ebe95f27e7b3252181fad50ce3a7ae3bd77b652742e0f4fb6f163cfd903d90dd4e701a29427509ca07615717c5e3d69912
-EBUILD rstudio-1.2.5033.ebuild 7183 BLAKE2B 38c0baa94c4c002dff6b5faf9ce7737832b74fc9de68d9077cc4e1f1a281a456023810a439d8a0b527d3e0ec6cd5860bac544bb30ab57d7077d22ffdb79fb875 SHA512 eb8460899577ddb1ac3925d42737fb8737798cd1b15f7c731283a4fc5b7e413101233325d15b56355d37aab1a27ef87266582c35771f04ab71e4f6714611cdd2
-EBUILD rstudio-1.2.5042.ebuild 7232 BLAKE2B 6bbc99764eb8e521bcf41cdc45a9d9e777a78d400c7feeb97d6c477c2b002678bca746680fbffedc8e894cbc2d6141dd032e68280f7766d7051a95add514bb1c SHA512 f5faf42857ec815aef7dc4ddc8e7672e0502e6d68fcc368fb334a58dc96c2a5372e73a6ce191920537b21126ad718b359469e7f7529c819e340cb6fa4f2a5168
+DIST rstudio-1.3.959.tar.gz 89639419 BLAKE2B d45b2c1b0e426ddb5a945e59a8127ddfd47f6230ef0929639c4b525382ae57437a273df6ade85cfbf3a29911cf0158ee2e0808bfa94e783d70d4615f6c228f31 SHA512 e5d8bfe16011790ff4723c731043f44070d8fe48f85c5a9ab8389c9a2b7a1d3813e9362063ec4c6a6ca3b0a0857e2190481cbb74191650a129c0d2e10b342fac
+EBUILD rstudio-1.2.5033.ebuild 7256 BLAKE2B 5b6481bbe0d02d6751ab19df0ac2a12e8d71399cb13999d65f1c6b0ce2fab49eb0ad7e55b458933d6c3fc2490f2ecc2a5e4e0c5b41c7e36a978bf825bc27f8c5 SHA512 14a307c42c979fb18c19ccf0bb68322d9382dba785421120c21c77aac666b0517e069cb60f408baa53c349c1f3b6f8ab2a59db442ec377a244ce462b395ddb1c
+EBUILD rstudio-1.2.5042.ebuild 7256 BLAKE2B 24303ced907ff45ff66fbab6638f7bda958849ae977e0b3f37e00eb396b7ff6169ae7e10b2285c804e9cec2131cce8d45bfa8197096774fef06fc859460c5aad SHA512 f5c36843edbd62a80891b1a148081e163254fcdbdc94aafd4c9051992d63704dc360c0ee129ba92b9cc0a63e39c8cf6be258606db3b1a8831f1ee8a7110ad08c
+EBUILD rstudio-1.3.959.ebuild 7047 BLAKE2B 78861c03e1b7aff68ba63cc00503e09eca8d67b77df12161f8bed33d226440fc70e76b584cfb4a6236836250791d6d50f127c57c9ffc36add95866db7b19ca5e SHA512 0ae6d91439d4fb22eb27d9e58d9d5bf05f6cb063e947f4431593f9cb5c60b85e9e817cd668cb1a5d8313d74ed6cb6f0136ef370a45ef4da7f1f17a9e7c8ba0ca
MISC metadata.xml 590 BLAKE2B 53dc62775e118c9c26ee05e20ee1da1ac31b6a6b74cf7dac410856fe4e0cce40fbb800c7a03e60f59e14442baf3aad866ad42616ad5fbb5724f7f6d8c1636eea SHA512 7111442aaa52da1e554c34f824113ec0e227798dd11b0ea9148b81e7a31c08b2a527b9995e3adb9363c7a4f2a8594f30cbd4a179545bf31d69f07d5558c20f52
diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch
deleted file mode 100644
index a336fccbc981..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Some gcc hardening options were added, however since we add
-"-Wl,--as-needed" we end up with "-Wl,--as-needed;-Wl,-z,relro" which
-leads to linker errors about unknown options, if we make it so the
-as-needed option is the last option on the line, everything is fine.
-
-diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
-index 0589ca0..fe5bd5f 100644
---- a/src/cpp/CMakeLists.txt
-+++ b/src/cpp/CMakeLists.txt
-@@ -57,7 +57,7 @@ if(UNIX)
- add_definitions(-D_FORTIFY_SOURCE=2)
- add_definitions(-fstack-protector --param ssp-buffer-size=4)
- add_definitions(-pie -fPIE)
-- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-z,relro,-z,now")
-+ set(CMAKE_EXE_LINKER_FLAGS "-Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
- endif()
-
- # Win32 specific global directives
diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
deleted file mode 100644
index 483613cc5c09..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
+++ /dev/null
@@ -1,45 +0,0 @@
---- rstudio-0.99.879-orig/src/gwt/build.xml 2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/gwt/build.xml 2016-02-20 00:25:39.458756693 +1100
-@@ -25,6 +25,7 @@
- <property name="gwt.extra.args" value=""/>
- <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
- <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+ <property environment="env"/>
-
- <path id="project.class.path">
- <pathelement location="bin"/>
-@@ -101,8 +102,10 @@
- <pathelement location="src"/>
- <path refid="project.class.path"/>
- </classpath>
-+ <jvmarg value="-Duser.home=${env.T}"/>
- <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
- <jvmarg value="-Xmx1536M"/>
-+ <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
- <arg value="-war"/>
- <arg value="www"/>
- <arg value="-localWorkers"/>
-@@ -142,6 +145,7 @@
- <pathelement location="src"/>
- <path refid="project.class.path"/>
- </classpath>
-+ <jvmarg value="-Duser.home=${env.T}"/>
- <jvmarg value="-Xmx2048M"/>
- <arg value="-war"/>
- <arg value="www"/>
-@@ -163,6 +167,7 @@
- <pathelement location="src"/>
- <path refid="project.class.path"/>
- </classpath>
-+ <jvmarg value="-Duser.home=${env.T}"/>
- <jvmarg value="-Xmx2048M"/>
- <arg value="-src"/>
- <arg value = "src"/>
-@@ -194,6 +199,7 @@
- <pathelement location="src"/>
- <path refid="test.class.path"/>
- </classpath>
-+ <jvmarg value="-Duser.home=${env.T}"/>
- <arg value="org.rstudio.studio.selenium.RStudioTestSuite"/>
- </java>
- </sequential>
diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
deleted file mode 100644
index b2a1a33b44c2..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
+++ /dev/null
@@ -1,130 +0,0 @@
---- rstudio-1.0.44-orig/CMakeGlobals.txt 2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/CMakeGlobals.txt 2016-12-01 23:33:04.149326324 +1100
-@@ -123,7 +123,7 @@
- else()
- set(RSTUDIO_INSTALL_BIN bin)
- endif()
-- set(RSTUDIO_INSTALL_SUPPORTING .)
-+ set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
-
- # if the install prefix is /usr/local then tweak as appropriate
---- rstudio-1.0.44-orig/src/cpp/server/CMakeLists.txt 2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/server/CMakeLists.txt 2016-12-01 23:35:51.634862018 +1100
-@@ -155,7 +155,7 @@
- configure_file(${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")
-@@ -163,7 +163,7 @@
- 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")
-@@ -171,13 +171,13 @@
- 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 apparmor profile
- set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -185,9 +185,9 @@
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
- ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
-- DESTINATION ${RSERVER_APPARMOR_DIR})
-+ DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
-- DESTINATION ${RSERVER_APPARMOR_DIR})
-+ DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-
- # install configured upstart profile
- set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -195,12 +195,12 @@
- 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-1.0.44-orig/src/cpp/server/ServerOptions.cpp 2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/server/ServerOptions.cpp 2016-12-01 23:33:04.151326331 +1100
-@@ -386,8 +386,8 @@
-
- // 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-1.0.44-orig/src/cpp/session/SessionOptions.cpp 2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/session/SessionOptions.cpp 2016-12-01 23:33:04.151326331 +1100
-@@ -49,7 +49,7 @@
- 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";
-
-@@ -481,14 +481,14 @@
- }
-
- // 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_);
-@@ -498,7 +498,7 @@
- resolvePath(resourcePath_, &sumatraPath_);
- resolvePath(resourcePath_, &winutilsPath_);
- #endif
-- 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-1.1.357-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
deleted file mode 100644
index 28b0220912a0..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-Index: rstudio-1.1.357/src/cpp/session/CMakeLists.txt
-===================================================================
---- rstudio-1.1.357.orig/src/cpp/session/CMakeLists.txt
-+++ rstudio-1.1.357/src/cpp/session/CMakeLists.txt
-@@ -25,9 +25,6 @@ endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
- message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
-- message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
-
- # we often install embedded versions of these packages but don't do so currently
-
-@@ -38,22 +35,6 @@ endif()
- # message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
- # endif()
-
--# verify libclang is installed
--if(WIN32)
-- set(LIBCLANG_VERSION "3.4")
--else()
-- set(LIBCLANG_VERSION "3.5")
--endif()
--set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
--if(NOT EXISTS "${LIBCLANG_DIR}")
-- message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found (re-run install-dependencies script to install)")
--endif()
--set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
--if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
-- message(FATAL_ERROR "libclang builtin-headers not found (re-run install-dependencies script to install)")
--endif()
--
--
- # include files
- file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
-
-@@ -465,13 +446,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
- install(DIRECTORY "resources/connections"
- DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
-
-- # install pandoc
-- set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.19.2.1")
-- file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
-- install(FILES ${PANDOC_FILES}
-- PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
-- DESTINATION ${RSTUDIO_INSTALL_BIN}/pandoc)
--
- # install rmarkdown package
- # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
- # install(FILES ${RMARKDOWN_PACKAGE}
-@@ -502,24 +476,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
- install(DIRECTORY "resources/profiler"
- DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
-
-- # install libclang
-- if(WIN32)
-- file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
-- install(PROGRAMS ${LIBCLANG_32_FILES}
-- DESTINATION ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
-- file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
-- install(PROGRAMS ${LIBCLANG_64_FILES}
-- DESTINATION ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
-- else()
-- file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
-- install(PROGRAMS ${LIBCLANG_FILES}
-- DESTINATION ${RSTUDIO_INSTALL_BIN}/rsclang)
-- endif()
--
-- # install libclang builtin-headers
-- install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
-- DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
--
- # install winpty on windows
- if(WIN32)
- install(PROGRAMS "${WINPTY_BINDIR_32}/winpty.dll"
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
deleted file mode 100644
index 760c9b561055..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- rstudio-1.1.453-orig/src/cpp/core/DateTime.cpp 2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/core/DateTime.cpp 2018-07-02 16:19:21.335703471 +1000
-@@ -65,7 +65,7 @@
- using namespace boost::posix_time;
-
- ptime time_t_epoch(date(1970,1,1));
-- return time_t_epoch + seconds(sec);
-+ return time_t_epoch + seconds(static_cast<long>(sec));
- }
-
- boost::posix_time::ptime timeFromMillisecondsSinceEpoch(int64_t ms)
---- rstudio-1.1.453-orig/src/cpp/core/file_lock/FileLock.cpp 2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/core/file_lock/FileLock.cpp 2018-07-02 17:00:35.915695201 +1000
-@@ -133,11 +133,11 @@
-
- // timeout interval
- double timeoutInterval = getFieldPositive(settings, "timeout-interval", kDefaultTimeoutInterval);
-- FileLock::s_timeoutInterval = boost::posix_time::seconds(timeoutInterval);
-+ FileLock::s_timeoutInterval = boost::posix_time::seconds(static_cast<long>(timeoutInterval));
-
- // refresh rate
- double refreshRate = getFieldPositive(settings, "refresh-rate", kDefaultRefreshRate);
-- FileLock::s_refreshRate = boost::posix_time::seconds(refreshRate);
-+ FileLock::s_refreshRate = boost::posix_time::seconds(static_cast<long>(refreshRate));
-
- // logging
- bool loggingEnabled = settings.getBool("enable-logging", false);
-@@ -212,8 +212,8 @@
-
- // default values for static members
- FileLock::LockType FileLock::s_defaultType(FileLock::LOCKTYPE_LINKBASED);
--boost::posix_time::seconds FileLock::s_timeoutInterval(kDefaultTimeoutInterval);
--boost::posix_time::seconds FileLock::s_refreshRate(kDefaultRefreshRate);
-+boost::posix_time::seconds FileLock::s_timeoutInterval(static_cast<long>(kDefaultTimeoutInterval));
-+boost::posix_time::seconds FileLock::s_refreshRate(static_cast<long>(kDefaultRefreshRate));
- bool FileLock::s_loggingEnabled(false);
- bool FileLock::s_isLoadBalanced(false);
- FilePath FileLock::s_logFile;
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
deleted file mode 100644
index a7a48572de30..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
+++ /dev/null
@@ -1,460 +0,0 @@
---- /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 @@
-+/*
-+ * BoostSignals.hpp
-+ *
-+ * Copyright (C) 2009-18 by RStudio, Inc.
-+ *
-+ * Unless you have received this program directly from RStudio pursuant
-+ * to the terms of a commercial license agreement with RStudio, then
-+ * this program is licensed to you under the terms of version 3 of the
-+ * GNU Affero General Public License. This program is distributed WITHOUT
-+ * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
-+ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
-+ * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
-+ *
-+ */
-+
-+#ifndef CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+#define CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+
-+#if RSTUDIO_BOOST_SIGNALS_VERSION == 1
-+
-+# include <boost/signals.hpp>
-+# define RSTUDIO_BOOST_SIGNAL boost::signal
-+# define RSTUDIO_BOOST_CONNECTION boost::signals::connection
-+# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals::scoped_connection
-+# define RSTUDIO_BOOST_LAST_VALUE boost::last_value
-+
-+#elif RSTUDIO_BOOST_SIGNALS_VERSION == 2
-+
-+# include <boost/signals2.hpp>
-+# define RSTUDIO_BOOST_SIGNAL boost::signals2::signal
-+# define RSTUDIO_BOOST_CONNECTION boost::signals2::connection
-+# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals2::scoped_connection
-+# define RSTUDIO_BOOST_LAST_VALUE boost::signals2::last_value
-+
-+#else
-+# error "Unrecognized RSTUDIO_BOOST_SIGNALS_VERSION"
-+#endif
-+
-+#endif // CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+
---- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/CMakeLists.txt 2018-11-17 21:24:35.285976284 +1100
-@@ -208,6 +208,18 @@
- message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
- endif()
-
-+# 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)
-+ set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
-+ else()
-+ set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
-+ endif()
-+endif()
-+
-+message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
-+add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
-
- # add boost as system include directory
- include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
---- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RConsoleHistory.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/include/r/session/RConsoleHistory.hpp 2018-11-17 21:24:35.285976284 +1100
-@@ -20,8 +20,8 @@
-
- #include <boost/utility.hpp>
- #include <boost/circular_buffer.hpp>
--#include <boost/signal.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
-
- namespace rstudio {
-@@ -44,7 +44,7 @@
- public:
- typedef boost::circular_buffer<std::string>::value_type value_type;
- typedef boost::circular_buffer<std::string>::const_iterator const_iterator;
-- typedef boost::signal<void (const std::string&)> AddSignal;
-+ typedef RSTUDIO_BOOST_SIGNAL<void (const std::string&)> AddSignal;
-
- private:
- ConsoleHistory();
-@@ -86,8 +86,7 @@
- core::Error loadFromFile(const core::FilePath& filePath, bool verifyFile);
- core::Error saveToFile(const core::FilePath& filePath) const;
-
-- boost::signals::connection connectOnAdd(
-- const AddSignal::slot_function_type& slot)
-+ RSTUDIO_BOOST_CONNECTION connectOnAdd(const AddSignal::slot_function_type& slot)
- {
- return onAdd_.connect(slot);
- }
---- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RGraphics.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/include/r/session/RGraphics.hpp 2018-11-17 21:24:35.286976293 +1100
-@@ -19,6 +19,8 @@
- #include <boost/system/error_code.hpp>
- #include <boost/date_time/posix_time/ptime.hpp>
-
-+#include <core/BoostSignals.hpp>
-+
- namespace rstudio {
- namespace r {
- namespace session {
-@@ -56,8 +58,8 @@
- #include <vector>
-
- #include <boost/function.hpp>
--#include <boost/signal.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/json/Json.hpp>
-
-@@ -162,7 +164,7 @@
- virtual void clear() = 0;
-
- // subscribe to showManipulator event
-- virtual boost::signal<void ()>& onShowManipulator() = 0;
-+ virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() = 0;
-
- // set manipulator values
- virtual void setPlotManipulatorValues(const core::json::Object& values) = 0;
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp 2018-11-17 21:24:35.286976293 +1100
-@@ -540,7 +540,7 @@
-
-
-
--boost::signal<void ()>& PlotManager::onShowManipulator()
-+RSTUDIO_BOOST_SIGNAL<void ()>& PlotManager::onShowManipulator()
- {
- return plotManipulatorManager().onShowManipulator();
- }
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp 2018-11-17 21:24:35.287976303 +1100
-@@ -22,10 +22,10 @@
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
- #include <boost/function.hpp>
--#include <boost/signal.hpp>
- #include <boost/regex.hpp>
- #include <boost/circular_buffer.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
-
-@@ -45,10 +45,10 @@
-
- struct GraphicsDeviceEvents
- {
-- boost::signal<void (SEXP)> onNewPage;
-- boost::signal<void ()> onDrawing;
-- boost::signal<void ()> onResized;
-- boost::signal<void ()> onClosed;
-+ RSTUDIO_BOOST_SIGNAL<void (SEXP)> onNewPage;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onDrawing;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onResized;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onClosed;
- };
-
- class PlotManipulatorManager;
-@@ -110,7 +110,7 @@
-
- virtual void clear();
-
-- virtual boost::signal<void ()>& onShowManipulator() ;
-+ virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
- virtual void setPlotManipulatorValues(const core::json::Object& values);
- virtual void manipulatorPlotClicked(int x, int y);
-
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp 2018-11-17 21:24:35.287976303 +1100
-@@ -184,7 +184,7 @@
- }
-
-
--boost::signal<void ()>& PlotManipulatorManager::onShowManipulator()
-+RSTUDIO_BOOST_SIGNAL<void ()>& PlotManipulatorManager::onShowManipulator()
- {
- return onShowManipulator_;
- }
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp 2018-11-17 21:24:35.287976303 +1100
-@@ -16,8 +16,7 @@
- #ifndef R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
- #define R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
-
--#include <boost/signal.hpp>
--
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/json/Json.hpp>
-
-@@ -53,7 +52,7 @@
- public:
- core::Error initialize(const UnitConversionFunctions& convert);
-
-- boost::signal<void ()>& onShowManipulator() ;
-+ RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
- void setPlotManipulatorValues(const core::json::Object& values);
- void manipulatorPlotClicked(int x, int y);
-
-@@ -85,7 +84,7 @@
- bool replayingManipulator_;
-
- // manipulator event hook
-- boost::signal<void ()> onShowManipulator_;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onShowManipulator_;
-
- // unit conversion function
- UnitConversionFunctions convert_;
---- rstudio-1.1.463-orig/src/cpp/server/include/server/ServerSessionManager.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/server/include/server/ServerSessionManager.hpp 2018-11-17 21:27:05.255436316 +1100
-@@ -20,9 +20,9 @@
- #include <vector>
- #include <map>
-
--#include <boost/signals.hpp>
- #include <boost/asio/io_service.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/Thread.hpp>
-
- #include <core/system/PosixSystem.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/SessionMain.cpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/SessionMain.cpp 2018-11-17 21:24:35.288976313 +1100
-@@ -33,12 +33,12 @@
- #include <boost/lexical_cast.hpp>
- #include <boost/format.hpp>
-
--#include <boost/signals.hpp>
- #include <boost/date_time/posix_time/posix_time.hpp>
- #include <boost/algorithm/string/predicate.hpp>
- #include <boost/algorithm/string/join.hpp>
-
- #include <core/Error.hpp>
-+#include <core/BoostSignals.hpp>
- #include <core/BoostThread.hpp>
- #include <core/ConfigUtils.hpp>
- #include <core/FilePath.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/SessionModuleContext.cpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/SessionModuleContext.cpp 2018-11-17 21:24:35.289976322 +1100
-@@ -19,10 +19,10 @@
-
- #include <boost/assert.hpp>
- #include <boost/utility.hpp>
--#include <boost/signal.hpp>
- #include <boost/format.hpp>
- #include <boost/numeric/conversion/cast.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/BoostThread.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
-@@ -586,13 +586,13 @@
-
- int nextGroup_;
-
-- boost::signal<void(const r::session::RSuspendOptions&,Settings*),
-- boost::last_value<void>,
-+ RSTUDIO_BOOST_SIGNAL<void(const r::session::RSuspendOptions&,Settings*),
-+ RSTUDIO_BOOST_LAST_VALUE<void>,
- int,
- std::less<int> > suspendSignal_;
-
-- boost::signal<void(const Settings&),
-- boost::last_value<void>,
-+ RSTUDIO_BOOST_SIGNAL<void(const Settings&),
-+ RSTUDIO_BOOST_LAST_VALUE<void>,
- int,
- std::greater<int> > resumeSignal_;
- };
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionConsoleProcess.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionConsoleProcess.hpp 2018-11-17 21:24:35.290976332 +1100
-@@ -20,10 +20,10 @@
- #include <deque>
-
- #include <boost/regex.hpp>
--#include <boost/signals.hpp>
- #include <boost/circular_buffer.hpp>
- #include <boost/enable_shared_from_this.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/system/Process.hpp>
- #include <core/terminal/PrivateCommand.hpp>
-
-@@ -146,7 +146,7 @@
- void setPromptHandler(
- const boost::function<bool(const std::string&, Input*)>& onPrompt);
-
-- boost::signal<void(int)>& onExit() { return onExit_; }
-+ RSTUDIO_BOOST_SIGNAL<void(int)>& onExit() { return onExit_; }
-
- std::string handle() const { return procInfo_->getHandle(); }
- InteractionMode interactionMode() const { return procInfo_->getInteractionMode(); }
-@@ -264,7 +264,7 @@
- boost::mutex inputOutputQueueMutex_;
-
- boost::function<bool(const std::string&, Input*)> onPrompt_;
-- boost::signal<void(int)> onExit_;
-+ RSTUDIO_BOOST_SIGNAL<void(int)> onExit_;
-
- // regex for prompt detection
- boost::regex controlCharsPattern_;
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionModuleContext.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionModuleContext.hpp 2018-11-17 21:28:25.019212857 +1100
-@@ -21,9 +21,9 @@
-
- #include <boost/utility.hpp>
- #include <boost/function.hpp>
--#include <boost/signals.hpp>
- #include <boost/shared_ptr.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/HtmlUtils.hpp>
- #include <core/system/System.hpp>
- #include <core/system/ShellUtils.hpp>
-@@ -315,35 +315,35 @@
- // session events
- struct Events : boost::noncopyable
- {
-- boost::signal<void (core::json::Object*)> onSessionInfo;
-- boost::signal<void ()> onClientInit;
-- boost::signal<void ()> onBeforeExecute;
-- boost::signal<void(const std::string&)> onConsolePrompt;
-- boost::signal<void(const std::string&)> onConsoleInput;
-- boost::signal<void(const std::string&, const std::string&)>
-+ RSTUDIO_BOOST_SIGNAL<void (core::json::Object*)> onSessionInfo;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onClientInit;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onBeforeExecute;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&)> onConsolePrompt;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&)> onConsoleInput;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)>
- onActiveConsoleChanged;
-- boost::signal<void (ConsoleOutputType, const std::string&)>
-+ RSTUDIO_BOOST_SIGNAL<void (ConsoleOutputType, const std::string&)>
- onConsoleOutput;
-- boost::signal<void()> onUserInterrupt;
-- boost::signal<void (ChangeSource)> onDetectChanges;
-- boost::signal<void (core::FilePath)> onSourceEditorFileSaved;
-- boost::signal<void(bool)> onDeferredInit;
-- boost::signal<void(bool)> afterSessionInitHook;
-- boost::signal<void(bool)> onBackgroundProcessing;
-- boost::signal<void(bool)> onShutdown;
-- boost::signal<void ()> onQuit;
-- boost::signal<void ()> onDestroyed;
-- boost::signal<void (const std::vector<std::string>&)>
-+ RSTUDIO_BOOST_SIGNAL<void()> onUserInterrupt;
-+ RSTUDIO_BOOST_SIGNAL<void (ChangeSource)> onDetectChanges;
-+ RSTUDIO_BOOST_SIGNAL<void (core::FilePath)> onSourceEditorFileSaved;
-+ RSTUDIO_BOOST_SIGNAL<void(bool)> onDeferredInit;
-+ RSTUDIO_BOOST_SIGNAL<void(bool)> afterSessionInitHook;
-+ RSTUDIO_BOOST_SIGNAL<void(bool)> onBackgroundProcessing;
-+ RSTUDIO_BOOST_SIGNAL<void(bool)> onShutdown;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onQuit;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onDestroyed;
-+ RSTUDIO_BOOST_SIGNAL<void (const std::vector<std::string>&)>
- onLibPathsChanged;
-- boost::signal<void (const std::string&)> onPackageLoaded;
-- boost::signal<void ()> onPackageLibraryMutated;
-- boost::signal<void ()> onPreferencesSaved;
-- boost::signal<void (const core::DistributedEvent&)>
-+ RSTUDIO_BOOST_SIGNAL<void (const std::string&)> onPackageLoaded;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onPackageLibraryMutated;
-+ RSTUDIO_BOOST_SIGNAL<void ()> onPreferencesSaved;
-+ RSTUDIO_BOOST_SIGNAL<void (const core::DistributedEvent&)>
- onDistributedEvent;
-- boost::signal<void (core::FilePath)> onPermissionsChanged;
-+ RSTUDIO_BOOST_SIGNAL<void (core::FilePath)> onPermissionsChanged;
-
- // signal for detecting extended type of documents
-- boost::signal<std::string(boost::shared_ptr<source_database::SourceDocument>),
-+ RSTUDIO_BOOST_SIGNAL<std::string(boost::shared_ptr<source_database::SourceDocument>),
- firstNonEmpty<std::string> > onDetectSourceExtendedType;
- };
-
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionSourceDatabase.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionSourceDatabase.hpp 2018-11-17 21:24:35.291976342 +1100
-@@ -21,8 +21,8 @@
-
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
--#include <boost/signals.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/FilePath.hpp>
- #include <core/json/Json.hpp>
-
-@@ -204,14 +204,14 @@
- // source database events
- struct Events : boost::noncopyable
- {
-- boost::signal<void(boost::shared_ptr<SourceDocument>)> onDocUpdated;
-- boost::signal<void(const std::string&,
-+ RSTUDIO_BOOST_SIGNAL<void(boost::shared_ptr<SourceDocument>)> onDocUpdated;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&,
- boost::shared_ptr<SourceDocument>)> onDocRenamed;
-- boost::signal<void(const std::string&)> onDocAdded;
-- boost::signal<void(
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&)> onDocAdded;
-+ RSTUDIO_BOOST_SIGNAL<void(
- boost::shared_ptr<source_database::SourceDocument>)> onDocPendingRemove;
-- boost::signal<void(const std::string&, const std::string&)> onDocRemoved;
-- boost::signal<void()> onRemoveAll;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)> onDocRemoved;
-+ RSTUDIO_BOOST_SIGNAL<void()> onRemoveAll;
- };
-
- Events& events();
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionUserSettings.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionUserSettings.hpp 2018-11-17 21:24:35.291976342 +1100
-@@ -20,8 +20,8 @@
-
- #include <boost/utility.hpp>
- #include <boost/scoped_ptr.hpp>
--#include <boost/signal.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/Settings.hpp>
- #include <core/FilePath.hpp>
- #include <core/StringUtils.hpp>
-@@ -62,7 +62,7 @@
- friend UserSettings& userSettings();
-
- public:
-- boost::signal<void()> onChanged;
-+ RSTUDIO_BOOST_SIGNAL<void()> onChanged;
-
- public:
- // COPYING: boost::noncopyable
---- rstudio-1.1.463-orig/src/cpp/session/include/session/projects/SessionProjects.hpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/projects/SessionProjects.hpp 2018-11-17 21:24:35.291976342 +1100
-@@ -22,8 +22,8 @@
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
- #include <boost/foreach.hpp>
--#include <boost/signals.hpp>
-
-+#include <core/BoostSignals.hpp>
- #include <core/FileInfo.hpp>
- #include <core/FilePath.hpp>
- #include <core/Settings.hpp>
-@@ -220,10 +220,10 @@
-
- bool hasFileMonitor_;
- std::vector<std::string> monitorSubscribers_;
-- boost::signal<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
-- boost::signal<void(const std::vector<core::system::FileChangeEvent>&)>
-+ RSTUDIO_BOOST_SIGNAL<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
-+ RSTUDIO_BOOST_SIGNAL<void(const std::vector<core::system::FileChangeEvent>&)>
- onFilesChanged_;
-- boost::signal<void()> onMonitoringDisabled_;
-+ RSTUDIO_BOOST_SIGNAL<void()> onMonitoringDisabled_;
- };
-
- ProjectContext& projectContext();
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
deleted file mode 100644
index d90ce005a1a0..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
+++ /dev/null
@@ -1,220 +0,0 @@
---- 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_p3.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
deleted file mode 100644
index 961723fd224f..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
+++ /dev/null
@@ -1,167 +0,0 @@
---- 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
deleted file mode 100644
index 320b823355a3..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- 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-1.1.463-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
deleted file mode 100644
index 914cd942e8f4..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- rstudio-1.1.463-orig/src/cpp/server/ServerSecureKeyFile.cpp 2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/server/ServerSecureKeyFile.cpp 2018-11-17 22:17:18.110012955 +1100
-@@ -79,8 +79,8 @@
- 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-boost-1.72-filesystem.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch
deleted file mode 100644
index b2c4d2392f6a..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From a11d0454e5fe9c50005a03b9d9de84355df5c7fd Mon Sep 17 00:00:00 2001
-From: Kevin Ushey <kevinushey@gmail.com>
-Date: Fri, 15 Nov 2019 14:54:02 -0800
-Subject: [PATCH] avoid use of deprecated APIs
-
----
- src/cpp/core/FilePath.cpp | 4 +---
- 1 file changed, 1 insertion(+), 3 deletions(-)
-
-diff --git a/src/cpp/shared_core/FilePath.cpp b/src/cpp/shared_core/FilePath.cpp
-index 088366a9d6..495289e7fc 100644
---- a/src/cpp/core/FilePath.cpp
-+++ b/src/cpp/core/FilePath.cpp
-@@ -22,8 +22,6 @@
- #include <windows.h>
- #endif
-
--#define BOOST_FILESYSTEM_NO_DEPRECATED
--
- #define BOOST_NO_CXX11_SCOPED_ENUMS
- #include <boost/filesystem.hpp>
- #undef BOOST_NO_CXX11_SCOPED_ENUMS
-@@ -1032,7 +1030,7 @@
- {
- // NOTE: The path gets round-tripped through toString/fromString, would
- // be nice to have a direct constructor
-- if (!iterationFunction(itr.level(),
-+ if (!iterationFunction(itr.depth(),
- FilePath(BOOST_FS_PATH2STR(itr->path()))))
- {
- // end the iteration if requested
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
deleted file mode 100644
index e38f5e0c4448..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- 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-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
deleted file mode 100644
index e2fe83867bcd..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- 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 ${RMARKDOWN_PACKAGE}
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
deleted file mode 100644
index e72df553eeb6..000000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- rstudio-1.2.1335-orig/src/gwt/build.xml 2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/gwt/build.xml 2019-04-09 16:44:15.089471934 +1000
-@@ -34,6 +34,7 @@
- <property name="gwt.extra.args" value=""/>
- <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
- <property name="ace.bin" value="${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-1.2.5042-R-4.0.0.patch b/sci-mathematics/rstudio/files/rstudio-1.2.5042-R-4.0.0.patch
new file mode 100644
index 000000000000..87ec83a7d4af
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.5042-R-4.0.0.patch
@@ -0,0 +1,106 @@
+From 71b1a935762efd24a79de193662450de5a89f67e Mon Sep 17 00:00:00 2001
+From: Jonathan McPherson <jonathan@rstudio.com>
+Date: Tue, 14 Jan 2020 12:53:20 -0800
+Subject: [PATCH] use R_NoSave over R_Slave for R 4.0+
+
+---
+ src/cpp/r/CMakeLists.txt | 12 ++++++++++++
+ src/cpp/r/config.h.in | 8 +++++++-
+ src/cpp/r/session/REmbeddedPosix.cpp | 20 ++++++++++++++------
+ 3 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/src/cpp/r/CMakeLists.txt b/src/cpp/r/CMakeLists.txt
+index 6984ae309c..29784b8b67 100644
+--- a/src/cpp/r/CMakeLists.txt
++++ b/src/cpp/r/CMakeLists.txt
+@@ -15,6 +15,18 @@
+
+ project (R)
+
++# find the version of R in play
++find_package(LibR REQUIRED)
++execute_process(
++ COMMAND "${LIBR_EXECUTABLE}" "--vanilla" "--slave" "-e" "cat(as.character(getRversion()))"
++ OUTPUT_VARIABLE LIBR_VERSION)
++
++# parse and save the R version to a variable
++string(REPLACE "." ";" R_VERSION_LIST "${LIBR_VERSION}")
++list(GET R_VERSION_LIST 0 R_VERSION_MAJOR)
++list(GET R_VERSION_LIST 1 R_VERSION_MINOR)
++list(GET R_VERSION_LIST 2 R_VERSION_PATCH)
++
+ # include files
+ file(GLOB_RECURSE R_HEADER_FILES "*.h*")
+
+diff --git a/src/cpp/r/config.h.in b/src/cpp/r/config.h.in
+index 6ba67c8e09..00bc8b6191 100644
+--- a/src/cpp/r/config.h.in
++++ b/src/cpp/r/config.h.in
+@@ -1,7 +1,7 @@
+ /*
+ * config.h.in
+ *
+- * Copyright (C) 2009-12 by RStudio, Inc.
++ * Copyright (C) 2009-20 by RStudio, Inc.
+ *
+ * Unless you have received this program directly from RStudio pursuant
+ * to the terms of a commercial license agreement with RStudio, then
+@@ -16,4 +16,10 @@
+
+ #cmakedefine PANGO_CAIRO_FOUND
+
++// Important: These variables represent the version of R found during
++// compile/link time, NOT the version of R present at runtime.
++#define R_VERSION_MAJOR ${R_VERSION_MAJOR}
++#define R_VERSION_MINOR ${R_VERSION_MINOR}
++#define R_VERSION_PATCH ${R_VERSION_PATCH}
++
+
+diff --git a/src/cpp/r/session/REmbeddedPosix.cpp b/src/cpp/r/session/REmbeddedPosix.cpp
+index ac71b94522..73e2e2ce7f 100644
+--- a/src/cpp/r/session/REmbeddedPosix.cpp
++++ b/src/cpp/r/session/REmbeddedPosix.cpp
+@@ -1,7 +1,7 @@
+ /*
+ * REmbeddedPosix.cpp
+ *
+- * Copyright (C) 2009-12 by RStudio, Inc.
++ * Copyright (C) 2009-20 by RStudio, Inc.
+ *
+ * Unless you have received this program directly from RStudio pursuant
+ * to the terms of a commercial license agreement with RStudio, then
+@@ -38,6 +38,8 @@ extern "C" void (*ptr_R_ProcessEvents)(void);
+ extern "C" typedef void (*ptr_QuartzCocoa_SetupEventLoop)(int, unsigned long);
+ #endif
+
++#include "config.h"
++
+ extern int R_running_as_main_program; // from unix/system.c
+
+ using namespace rstudio::core;
+@@ -103,14 +105,20 @@ void runEmbeddedR(const core::FilePath& /*rHome*/, // ignored on posix
+ //
+ structRstart rp;
+ Rstart Rp = &rp;
+- R_DefParams(Rp) ;
+- Rp->R_Slave = FALSE ;
++ R_DefParams(Rp);
++#if R_VERSION_MAJOR > 3
++ // R 4.0 and above use --no-echo to suppress output
++ Rp->R_NoEcho = FALSE;
++#else
++ // R 3.x and below use --slave
++ Rp->R_Slave = FALSE;
++#endif
+ Rp->R_Quiet = quiet ? TRUE : FALSE;
+- Rp->R_Interactive = TRUE ;
+- Rp->SaveAction = defaultSaveAction ;
++ Rp->R_Interactive = TRUE;
++ Rp->SaveAction = defaultSaveAction;
+ Rp->RestoreAction = SA_NORESTORE; // handled within initialize()
+ Rp->LoadInitFile = loadInitFile ? TRUE : FALSE;
+- R_SetParams(Rp) ;
++ R_SetParams(Rp);
+
+ // redirect console
+ R_Interactive = TRUE; // should have also been set by call to Rf_initialize_R
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
new file mode 100644
index 000000000000..dc35d0ce0083
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
@@ -0,0 +1,106 @@
+From 71b1a935762efd24a79de193662450de5a89f67e Mon Sep 17 00:00:00 2001
+From: Jonathan McPherson <jonathan@rstudio.com>
+Date: Tue, 14 Jan 2020 12:53:20 -0800
+Subject: [PATCH] use R_NoSave over R_Slave for R 4.0+
+
+---
+ src/cpp/r/CMakeLists.txt | 12 ++++++++++++
+ src/cpp/r/config.h.in | 8 +++++++-
+ src/cpp/r/session/REmbeddedPosix.cpp | 20 ++++++++++++++------
+ 3 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/src/cpp/r/CMakeLists.txt b/src/cpp/r/CMakeLists.txt
+index 6984ae309c..29784b8b67 100644
+--- a/src/cpp/r/CMakeLists.txt
++++ b/src/cpp/r/CMakeLists.txt
+@@ -15,6 +15,18 @@
+
+ project (R)
+
++# find the version of R in play
++find_package(LibR REQUIRED)
++execute_process(
++ COMMAND "${LIBR_EXECUTABLE}" "--vanilla" "--slave" "-e" "cat(as.character(getRversion()))"
++ OUTPUT_VARIABLE LIBR_VERSION)
++
++# parse and save the R version to a variable
++string(REPLACE "." ";" R_VERSION_LIST "${LIBR_VERSION}")
++list(GET R_VERSION_LIST 0 R_VERSION_MAJOR)
++list(GET R_VERSION_LIST 1 R_VERSION_MINOR)
++list(GET R_VERSION_LIST 2 R_VERSION_PATCH)
++
+ # include files
+ file(GLOB_RECURSE R_HEADER_FILES "*.h*")
+
+diff --git a/src/cpp/r/config.h.in b/src/cpp/r/config.h.in
+index 6ba67c8e09..00bc8b6191 100644
+--- a/src/cpp/r/config.h.in
++++ b/src/cpp/r/config.h.in
+@@ -1,7 +1,7 @@
+ /*
+ * config.h.in
+ *
+- * Copyright (C) 2009-12 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+ *
+ * Unless you have received this program directly from RStudio pursuant
+ * to the terms of a commercial license agreement with RStudio, then
+@@ -16,4 +16,10 @@
+
+ #cmakedefine PANGO_CAIRO_FOUND
+
++// Important: These variables represent the version of R found during
++// compile/link time, NOT the version of R present at runtime.
++#define R_VERSION_MAJOR ${R_VERSION_MAJOR}
++#define R_VERSION_MINOR ${R_VERSION_MINOR}
++#define R_VERSION_PATCH ${R_VERSION_PATCH}
++
+
+diff --git a/src/cpp/r/session/REmbeddedPosix.cpp b/src/cpp/r/session/REmbeddedPosix.cpp
+index ac71b94522..73e2e2ce7f 100644
+--- a/src/cpp/r/session/REmbeddedPosix.cpp
++++ b/src/cpp/r/session/REmbeddedPosix.cpp
+@@ -1,7 +1,7 @@
+ /*
+ * REmbeddedPosix.cpp
+ *
+- * Copyright (C) 2009-19 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+ *
+ * Unless you have received this program directly from RStudio pursuant
+ * to the terms of a commercial license agreement with RStudio, then
+@@ -38,6 +38,8 @@ extern "C" void (*ptr_R_ProcessEvents)(void);
+ extern "C" typedef void (*ptr_QuartzCocoa_SetupEventLoop)(int, unsigned long);
+ #endif
+
++#include "config.h"
++
+ extern int R_running_as_main_program; // from unix/system.c
+
+ using namespace rstudio::core;
+@@ -103,14 +105,20 @@ void runEmbeddedR(const core::FilePath& /*rHome*/, // ignored on posix
+ //
+ structRstart rp;
+ Rstart Rp = &rp;
+- R_DefParams(Rp) ;
+- Rp->R_Slave = FALSE ;
++ R_DefParams(Rp);
++#if R_VERSION_MAJOR > 3
++ // R 4.0 and above use --no-echo to suppress output
++ Rp->R_NoEcho = FALSE;
++#else
++ // R 3.x and below use --slave
++ Rp->R_Slave = FALSE;
++#endif
+ Rp->R_Quiet = quiet ? TRUE : FALSE;
+- Rp->R_Interactive = TRUE ;
+- Rp->SaveAction = defaultSaveAction ;
++ Rp->R_Interactive = TRUE;
++ Rp->SaveAction = defaultSaveAction;
+ Rp->RestoreAction = SA_NORESTORE; // handled within initialize()
+ Rp->LoadInitFile = loadInitFile ? TRUE : FALSE;
+- R_SetParams(Rp) ;
++ R_SetParams(Rp);
+
+ // redirect console
+ R_Interactive = TRUE; // should have also been set by call to Rf_initialize_R
diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
index 641f7710167a..0f6af4ef7f12 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
@@ -1,6 +1,31 @@
---- rstudio-1.1.453-orig/src/cpp/session/SessionClientInit.cpp 2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/session/SessionClientInit.cpp 2018-07-02 20:21:41.595654877 +1000
-@@ -105,7 +105,7 @@
+--- rstudio-1.3.959-orig/src/cpp/session/SessionClientInit.cpp 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionClientInit.cpp 2020-05-24 17:21:56.960469575 +1000
+@@ -91,13 +91,13 @@
+ 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;
+
+@@ -143,7 +143,7 @@
+ if (options.programMode() == kSessionProgramModeServer &&
+ !core::http::validateCSRFHeaders(ptrConnection->request()))
+ {
+- ptrConnection->sendJsonRpcError(Error(json::errc::Unauthorized, ERROR_LOCATION));
++ ptrConnection->sendJsonRpcError(Error(core::json::errc::Unauthorized, ERROR_LOCATION));
+ return;
+ }
+
+@@ -173,12 +173,12 @@
}
// prepare session info
@@ -8,8 +33,14 @@
+ core::json::Object sessionInfo ;
sessionInfo["clientId"] = clientId;
sessionInfo["mode"] = options.programMode();
-
-@@ -119,8 +119,8 @@
+
+ // build initialization options for client
+- json::Object initOptions;
++ core::json::Object initOptions;
+ initOptions["restore_workspace"] = options.rRestoreWorkspace();
+ initOptions["run_rprofile"] = options.rRunRprofile();
+ sessionInfo["init_options"] = initOptions;
+@@ -194,8 +194,8 @@
}
// temp dir
@@ -19,8 +50,8 @@
+ core::Error error = tempDir.ensureDirectory();
if (error)
LOG_ERROR(error);
- sessionInfo["temp_dir"] = tempDir.absolutePath();
-@@ -132,12 +132,12 @@
+ sessionInfo["temp_dir"] = tempDir.getAbsolutePath();
+@@ -213,12 +213,12 @@
sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
// client state
@@ -35,7 +66,7 @@
error = modules::source::clientInitDocuments(&jsonDocs);
if (error)
LOG_ERROR(error);
-@@ -159,7 +159,7 @@
+@@ -243,7 +243,7 @@
if (resumed)
{
// console actions
@@ -44,7 +75,7 @@
consoleActions.asJson(&actionsObject);
sessionInfo["console_actions"] = actionsObject;
}
-@@ -211,12 +211,12 @@
+@@ -310,12 +310,12 @@
}
else
{
@@ -60,24 +91,24 @@
+ sessionInfo["project_user_data_directory"] = core::json::Value();
}
- sessionInfo["system_encoding"] = std::string(::locale2charset(NULL));
-@@ -253,20 +253,20 @@
+ sessionInfo["system_encoding"] = std::string(::locale2charset(nullptr));
+@@ -352,20 +352,20 @@
sessionInfo["build_tools_bookdown_website"] =
module_context::isBookdownWebsite();
- FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+ core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
- if (!buildTargetDir.empty())
+ if (!buildTargetDir.isEmpty())
{
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();
+ buildTargetDir.completeChildPath("src").exists();
sessionInfo["has_pkg_vig"] =
- (type == r_util::kBuildTypePackage) &&
+ (type == core::r_util::kBuildTypePackage) &&
- buildTargetDir.childPath("vignettes").exists();
+ buildTargetDir.completeChildPath("vignettes").exists();
}
else
{
@@ -86,7 +117,7 @@
sessionInfo["has_pkg_src"] = false;
sessionInfo["has_pkg_vig"] = false;
}
-@@ -274,9 +274,9 @@
+@@ -373,9 +373,9 @@
}
else
{
@@ -98,7 +129,7 @@
sessionInfo["has_pkg_src"] = false;
sessionInfo["has_pkg_vig"] = false;
}
-@@ -285,7 +285,7 @@
+@@ -384,7 +384,7 @@
sessionInfo["presentation_commands"] = options.allowPresentationCommands();
sessionInfo["tutorial_api_available"] = false;
@@ -107,7 +138,7 @@
sessionInfo["build_state"] = modules::build::buildStateAsJson();
sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
-@@ -296,7 +296,7 @@
+@@ -395,7 +395,7 @@
// console history -- we do this at the end because
// restoreBuildRestartContext may have reset it
@@ -116,13 +147,14 @@
rstudio::r::session::consoleHistory().asJson(&historyArray);
sessionInfo["console_history"] = historyArray;
sessionInfo["console_history_capacity"] =
-@@ -364,13 +364,13 @@
+@@ -470,14 +470,14 @@
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;
@@ -132,12 +164,21 @@
sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
-@@ -394,7 +394,7 @@
+@@ -501,7 +501,7 @@
- // send response (we always set kEventsPending to false so that the client
+ sessionInfo["launcher_jobs_enabled"] = modules::overlay::launcherJobsFeatureDisplayed();
+
+- json::Object packageDependencies;
++ core::json::Object packageDependencies;
+ error = modules::dependency_list::getDependencyList(&packageDependencies);
+ if (error)
+ LOG_ERROR(error);
+@@ -529,7 +529,7 @@
+
+ // 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 ;
+- json::JsonRpcResponse jsonRpcResponse;
++ core::json::JsonRpcResponse jsonRpcResponse;
jsonRpcResponse.setField(kEventsPending, "false");
- jsonRpcResponse.setResult(sessionInfo) ;
- ptrConnection->sendJsonRpcResponse(jsonRpcResponse);
+ jsonRpcResponse.setResult(sessionInfo);
+
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
new file mode 100644
index 000000000000..d8718dda9b18
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
@@ -0,0 +1,42 @@
+--- rstudio-1.3.959-orig/src/cpp/session/CMakeLists.txt 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/CMakeLists.txt 2020-05-24 18:54:40.444955162 +1000
+@@ -22,12 +22,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
+ message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27")
+- message(FATAL_ERROR "Mathjax 2.7 not found (re-run install-dependencies script to install)")
+-endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+- message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+
+ # verify embedded packages are available
+ foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+@@ -500,10 +494,6 @@
+ install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries"
+ DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+
+- # install mathjax for local html preview
+- install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27"
+- DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+-
+ # icons for database connections
+ install(DIRECTORY "resources/connections"
+ DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+@@ -516,15 +506,6 @@
+ install(DIRECTORY "resources/dependencies"
+ DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+
+- # install pandoc
+- set(PANDOC_VERSION "2.7.3" CACHE INTERNAL "Pandoc version")
+-
+- set(PANDOC_BIN "${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 embedded packages
+ foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+ file(GLOB PKG_FILES "${RSTUDIO_DEPENDENCIES_DIR}/common/${PKG}*.tar.gz")
diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
index ba66ef9f0ea1..175d52f7149a 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
@@ -1,17 +1,17 @@
---- 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)
+--- rstudio-1.3.959-orig/CMakeGlobals.txt 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/CMakeGlobals.txt 2020-05-25 19:30:10.711859714 +1000
+@@ -181,7 +181,7 @@
+ else()
+ set(RSTUDIO_INSTALL_BIN bin)
+ endif()
- set(RSTUDIO_INSTALL_SUPPORTING .)
+ set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
endif()
# if the install prefix is /usr/local then tweak as appropriate
---- rstudio-1.2.1335-orig/src/cpp/server/CMakeLists.txt 2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/server/CMakeLists.txt 2019-04-09 16:54:34.740739744 +1000
-@@ -194,7 +194,7 @@
+--- rstudio-1.3.959-orig/src/cpp/server/CMakeLists.txt 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/CMakeLists.txt 2020-05-25 19:30:10.711859714 +1000
+@@ -190,7 +190,7 @@
configure_file(${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}
@@ -20,7 +20,7 @@
# install configured redhat init.d script
set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -202,7 +202,7 @@
+@@ -198,7 +198,7 @@
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}
@@ -29,7 +29,7 @@
# install configured suse init.d script
set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -210,13 +210,13 @@
+@@ -206,13 +206,13 @@
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}
@@ -45,7 +45,7 @@
# install configured upstart profile
set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -224,12 +224,12 @@
+@@ -220,12 +220,12 @@
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}
@@ -60,22 +60,22 @@
# 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 @@
+--- rstudio-1.3.959-orig/src/cpp/server/ServerOptions.cpp 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/ServerOptions.cpp 2020-05-25 19:34:19.377675880 +1000
+@@ -442,8 +442,8 @@
// 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(resourcePath.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++ resolvePath(resourcePath.completeChildPath(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 @@
+--- rstudio-1.3.959-orig/src/cpp/session/SessionOptions.cpp 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionOptions.cpp 2020-05-25 19:33:58.318606745 +1000
+@@ -52,7 +52,7 @@
namespace session {
namespace {
@@ -84,7 +84,7 @@
const char* const kDefaultPostbackPath = "bin/postback/rpostback";
const char* const kDefaultRsclangPath = "bin/rsclang";
-@@ -569,14 +569,14 @@
+@@ -586,14 +586,14 @@
}
// convert relative paths by completing from the app resource path
@@ -96,23 +96,23 @@
- 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_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &rResourcesPath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &agreementFilePath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &coreRSourcePath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &modulesRSourcePath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionLibraryPath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
resolvePostbackPath(resourcePath_, &rpostbackPath_);
#ifdef _WIN32
resolvePath(resourcePath_, &consoleIoPath_);
-@@ -601,7 +601,7 @@
+@@ -626,7 +626,7 @@
}
- winptyPath_ = pty.complete(completion).absolutePath();
+ winptyPath_ = pty.completePath(completion).getAbsolutePath();
#endif // _WIN32
- resolvePath(resourcePath_, &hunspellDictionariesPath_);
-+ resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
++ resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &hunspellDictionariesPath_);
resolvePath(resourcePath_, &mathjaxPath_);
resolvePath(resourcePath_, &libclangHeadersPath_);
resolvePandocPath(resourcePath_, &pandocPath_);
diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
new file mode 100644
index 000000000000..4f9613947694
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
@@ -0,0 +1,68 @@
+--- rstudio-1.3.959-orig/src/gwt/build.xml 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/gwt/build.xml 2020-05-25 17:38:28.911881424 +1000
+@@ -28,19 +28,37 @@
+ classname="com.google.javascript.jscomp.ant.CompileTask"
+ classpath="${tools.dir}/compiler/compiler.jar"/>
+
++ <!-- Configure path to aopalliance -->
++ <property name="aopalliance.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/aopalliance-1/lib"/>
++
++ <!-- Configure path to javax-inject -->
++ <property name="javax.inject" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/javax-inject/lib"/>
++
++ <!-- Configure path to validation-api -->
++ <property name="validation.api" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/lib"/>
++ <property name="validation.api.sources" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/sources"/>
++
+ <!-- Configure path to GWT SDK -->
+ <property name="gwt.sdk" value="${lib.dir}/gwt/gwt-rstudio-1.3"/>
++ <!-- Configure path to Google Gin -->
++ <property name="gin.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/gin-2.1/lib"/>
++
+ <property name="gwt.extra.args" value=""/>
+ <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+ <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++ <property environment="env"/>
+
+ <!-- configure code server -->
+ <property name="bind.address" value="127.0.0.1"/>
+
+ <path id="project.class.path">
+ <pathelement location="${build.dir}"/>
++ <fileset dir="${aopalliance.sdk}" includes="*.jar"/>
++ <fileset dir="${javax.inject}" includes="*.jar"/>
++ <fileset dir="${validation.api}" includes="*.jar"/>
++ <fileset dir="${validation.api.sources}" includes="*.zip"/>
+ <fileset dir="${gwt.sdk}" includes="*.jar"/>
+- <fileset dir="${lib.dir}/gin/2.1.2" includes="*.jar"/>
++ <fileset dir="${gin.sdk}" includes="*.jar"/>
+ </path>
+
+ <path id="test.class.path">
+@@ -114,8 +132,10 @@
+ <pathelement location="${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="${www.dir}"/>
+ <arg value="-localWorkers"/>
+@@ -168,6 +188,7 @@
+ <pathelement location="${src.dir}"/>
+ <path refid="project.class.path"/>
+ </classpath>
++ <jvmarg value="-Duser.home=${env.T}"/>
+ <jvmarg value="-Xmx2048M"/>
+ <arg value="-style"/>
+ <arg value="PRETTY"/>
+@@ -212,6 +233,7 @@
+ <pathelement location="${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-0.99.473-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
index bf66bd236788..3ced4f9afa1c 100644
--- a/sci-mathematics/rstudio/files/rstudio-0.99.473-qtsingleapplication.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
@@ -1,20 +1,20 @@
---- rstudio-0.99.473-orig/src/cpp/desktop/CMakeLists.txt 2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/desktop/CMakeLists.txt 2015-08-30 23:16:11.396175587 +1000
-@@ -93,7 +93,12 @@
- find_package(Qt5DBus REQUIRED)
- endif()
+--- rstudio-1.3.959-orig/src/cpp/desktop/CMakeLists.txt 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/CMakeLists.txt 2020-05-24 17:15:47.039422975 +1000
+@@ -138,6 +138,13 @@
+ 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)
-@@ -113,7 +118,6 @@
+ add_definitions(-Wno-unused-private-field
+@@ -156,7 +163,6 @@
set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
@@ -22,33 +22,33 @@
${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
-@@ -175,8 +179,6 @@
- DesktopSubMenu.cpp
+@@ -225,8 +231,6 @@
DesktopSynctex.cpp
- DesktopNetworkAccessManager.cpp
+ DesktopJobLauncherOverlay.cpp
+ RemoteDesktopSessionLauncherOverlay.cpp
- 3rdparty/qtsingleapplication/qtsingleapplication.cpp
- 3rdparty/qtsingleapplication/qtlocalpeer.cpp
)
if(WIN32)
-@@ -219,6 +221,7 @@
- ${CORE_SOURCE_DIR}/include
+@@ -283,6 +287,7 @@
+ ${OPENSSL_INCLUDE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
+ ${QTSINGLEAPPLIB_INCLUDE_DIR}
+ ${EXT_SOURCE_DIR}
+ ${SESSION_SOURCE_DIR}/include
${TESTS_INCLUDE_DIR}
- )
-
-@@ -332,6 +335,7 @@
-
+@@ -386,6 +391,7 @@
# set link dependencies
target_link_libraries(rstudio
+ ${RSTUDIO_QTMODULES}
+ ${QTSINGLEAPPLIB}
${QT_LIBRARIES}
+ ${Boost_LIBRARIES}
rstudio-core
- ${LINK_FLAGS}
---- rstudio-0.99.473-orig/src/cpp/desktop/DesktopPosixApplication.hpp 2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/desktop/DesktopPosixApplication.hpp 2015-08-30 21:41:21.616934106 +1000
+--- rstudio-1.3.959-orig/src/cpp/desktop/DesktopPosixApplication.hpp 2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/DesktopPosixApplication.hpp 2020-05-24 17:13:22.050016953 +1000
@@ -16,7 +16,7 @@
#ifndef DESKTOP_POSIX_APPLICATION_HPP
#define DESKTOP_POSIX_APPLICATION_HPP
@@ -56,5 +56,5 @@
-#include "3rdparty/qtsingleapplication/QtSingleApplication"
+#include <QtSingleApplication>
- namespace rstudio {
- namespace desktop {
+ #include "DesktopApplicationLaunch.hpp"
+
diff --git a/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
deleted file mode 100644
index 8b60b2efe5b7..000000000000
--- a/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
+++ /dev/null
@@ -1,255 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils vcs-clean
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
-PANDOC_VER=1.19.2.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
- http://www.rstudio.org
- https://github.com/rstudio/rstudio/"
-SRC_URI="
- https://github.com/rstudio/rstudio/archive/v${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? ( sys-libs/pam )
- )
- dedicated? ( sys-libs/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 "${FILESDIR}"/rsession.conf
- dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
- if use dedicated || use server; then
- dopamd src/cpp/server/extras/pam/rstudio
- newinitd "${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-1.2.5033.ebuild b/sci-mathematics/rstudio/rstudio-1.2.5033.ebuild
index 88b8f9d905b8..09ff6e9c5162 100644
--- a/sci-mathematics/rstudio/rstudio-1.2.5033.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.2.5033.ebuild
@@ -99,6 +99,8 @@ PATCHES=(
"${FILESDIR}"/${PN}-1.2.1335-core.patch
"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p1.patch
"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p2.patch
+ "${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+ "${FILESDIR}"/${PN}-1.2.5042-R-4.0.0.patch
)
src_unpack() {
@@ -208,7 +210,6 @@ src_install() {
cmake-utils_src_install
use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
doconfd "${FILESDIR}"/rstudio-server.conf
- dodir /etc/rstudio
insinto /etc/rstudio
doins "${FILESDIR}"/rsession.conf
dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
diff --git a/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild b/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild
index 2de83f6f633f..6c4943d4513b 100644
--- a/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.2.5042.ebuild
@@ -100,6 +100,7 @@ PATCHES=(
"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p1.patch
"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p2.patch
"${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+ "${FILESDIR}"/${PN}-1.2.5042-R-4.0.0.patch
)
src_unpack() {
@@ -209,7 +210,6 @@ src_install() {
cmake-utils_src_install
use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
doconfd "${FILESDIR}"/rstudio-server.conf
- dodir /etc/rstudio
insinto /etc/rstudio
doins "${FILESDIR}"/rsession.conf
dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
diff --git a/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild b/sci-mathematics/rstudio/rstudio-1.3.959.ebuild
index 2ba27bd51487..d708ec5bd513 100644
--- a/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.3.959.ebuild
@@ -1,29 +1,21 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 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 vcs-clean
+inherit eutils cmake-utils pam xdg-utils java-pkg-2 java-ant-2 pax-utils prefix qmake-utils vcs-clean
# 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
+# It should be PANDOC_VER=2.7.3 however >=app-text/pandoc-2.7.3 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
+# grep -5 QT_CANDIDATES src/cpp/desktop/CMakeLists.txt
+QT_VER=5.12.6
+QT_SLOT=5
DESCRIPTION="IDE for the R language"
HOMEPAGE="
@@ -31,16 +23,7 @@ HOMEPAGE="
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_${RSCONNECT_VER}.tar.gz
"
LICENSE="AGPL-3"
@@ -48,16 +31,18 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="dedicated libressl server"
-QT_VER=5.4
-QT_SLOT=5
RDEPEND="
>=app-text/pandoc-${PANDOC_VER}
+ dev-java/aopalliance:1
+ dev-java/gin:2.1
+ dev-java/javax-inject
+ =dev-java/validation-api-1.0*:1.0[source]
dev-haskell/pandoc-citeproc
- >=dev-lang/R-2.11.1
- >=dev-libs/boost-1.63:=
+ dev-lang/R
+ dev-libs/boost:=
>=dev-libs/mathjax-2.7.4
sys-apps/util-linux
- >=sys-devel/clang-3.5.0:*
+ sys-devel/clang:*
sys-libs/zlib
>=virtual/jre-1.8:=
x11-libs/pango
@@ -82,6 +67,15 @@ RDEPEND="
server? ( sys-libs/pam )
)
dedicated? ( sys-libs/pam )
+ dedicated? (
+ sys-libs/pam
+ acct-user/rstudio-server
+ acct-group/rstudio-server
+ )
+ server? (
+ acct-user/rstudio-server
+ acct-group/rstudio-server
+ )
!libressl? ( dev-libs/openssl:0= )
libressl? ( dev-libs/libressl:0= )"
DEPEND="${RDEPEND}
@@ -92,50 +86,23 @@ DEPEND="${RDEPEND}
# 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}-1.3.959-prefs.patch
+ "${FILESDIR}"/${PN}-1.3.959-paths.patch
+ "${FILESDIR}"/${PN}-1.3.959-pandoc-mathjax.patch
"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
- "${FILESDIR}"/${PN}-1.2.1335-qtsingleapplication.patch
+ "${FILESDIR}"/${PN}-1.3.959-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
- "${FILESDIR}"/${PN}-1.2.1335-boost-1.72-filesystem.patch
+ "${FILESDIR}"/${PN}-1.3.959-core.patch
+ "${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+ "${FILESDIR}"/${PN}-1.3.959-R-4.0.0.patch
)
src_unpack() {
- unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+ unpack ${P}.tar.gz
cd "${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-${GIN_VER}.zip || die
+ mkdir -p dependencies/common/dictionaries
unzip -qd dependencies/common/dictionaries \
"${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() {
@@ -162,6 +129,11 @@ src_prepare() {
-e "s:/usr:${EPREFIX}/usr:g" \
CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+ # install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes
+ sed -i \
+ -e "s@\(DESTINATION \"\)\(extras/themes\"\)@\1${EROOT}/etc/rstudio/\2@" \
+ src/cpp/server/CMakeLists.txt || die
+
# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
-i src/cpp/server/ServerOptions.cpp \
@@ -187,10 +159,12 @@ src_prepare() {
|| die
# The git commit for tag: git rev-list -n 1 v${PV}
- sed -e 's@git ARGS rev-parse HEAD@echo ARGS 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
+ sed -e 's@git ARGS rev-parse HEAD@echo ARGS 3a09be39fd51a8fafa8ae330007937d31924b395@'\
-i "${S}"/CMakeLists.txt \
"${S}"/CMakeGlobals.txt \
|| die
+
+ eprefixify src/gwt/build.xml
}
src_configure() {
@@ -200,16 +174,26 @@ src_configure() {
local mycmakeargs=(
-DDISTRO_SHARE=share/${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
+ -DRSTUDIO_USE_SYSTEM_BOOST=TRUE
)
+ if use !dedicated; then
+ mycmakeargs+=(
+ -DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+ -DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+ )
+ fi
cmake-utils_src_configure
}
src_compile() {
+ local JAVA_ANT_REWRITE_CLASSPATH="yes"
+ local EANT_BUILD_XML="src/gwt/build.xml"
+ local EANT_BUILD_TARGET="clean"
+ java-pkg-2_src_compile
+
# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
# P: /root/.oracle_jre_usage.
export ANT_OPTS="-Duser.home=${T}"
@@ -219,9 +203,8 @@ src_compile() {
src_install() {
export ANT_OPTS="-Duser.home=${T}"
cmake-utils_src_install
- pax-mark m "${ED}/usr/bin/rstudio"
+ use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
doconfd "${FILESDIR}"/rstudio-server.conf
- dodir /etc/rstudio
insinto /etc/rstudio
doins "${FILESDIR}"/rsession.conf
dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
@@ -232,23 +215,17 @@ src_install() {
}
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
+ xdg_icon_cache_update ;}
}
pkg_postrm() {
use dedicated || { xdg_desktop_database_update
xdg_mimeinfo_database_update
- gnome2_icon_cache_update ;}
+ xdg_icon_cache_update ;}
}
diff --git a/sci-mathematics/rw/Manifest b/sci-mathematics/rw/Manifest
index 86b3e0904e57..37073adb4728 100644
--- a/sci-mathematics/rw/Manifest
+++ b/sci-mathematics/rw/Manifest
@@ -1,3 +1,4 @@
DIST rw-0.8.tar.gz 217215 BLAKE2B e6f379ce7cde0fafb0c6e234e8958018c0682ad47e60da3755a891b7eee4c910e84556252a333a12fe0cf2eac88863a272cb8fa6d2cfa4c9f1e93bd88bc6a2d2 SHA512 609d46fd3c76e2eb1724cc3e3ff9354d13b3c15ce23b96bef9f73f02b490e1d8713146230db079fcc87f45f5acc0e04130dac04e27589836e20891c63219f3ec
EBUILD rw-0.8-r2.ebuild 995 BLAKE2B f9b78b421a24cedc9a347f63b22e5b33d8cf115121724705207fae590c303d1956b2001f91e3735332b748ef189fafeb42d04f6844a66881790152babc76cfb5 SHA512 2fd5999820443b7d755814af961b1e1c862749180ffc6c3815be15cdc3790c036a2de5c4e4a02d5bf316c7cb1e0b6b024c86484a0a6022b831ba91ba73554660
+EBUILD rw-0.8-r3.ebuild 1125 BLAKE2B aa92fd85cde10922d0979d0503d0a4ff4e51372f15e5a5a17299d96938fdc010c5206302dbbacf5662b1536c1c8b990dae0512e00daef1eb4897d762d5d2f394 SHA512 20c39b004d9d25ebc34a35a9907f3173e554923a78eaaee3da2be0c8a991aa6099f758fb465731b43c35abd18296e2c05d974d1680c2735c5f43b29cbb08e9bb
MISC metadata.xml 1128 BLAKE2B 30c263e8a47107c0c5d9a7ee5377a5deaa6260767734361b85eca07f5c1a88d8f2375f2c5d20a28cd1241fcf70a2dfcff16a7fc2886977dfd9f25b5388aa73bb SHA512 34ec83d5cf7d7ed12ef6c58291a6a1b8323d580121e8b489dadc569f09b184e6952cefd934da504542a7a4cbe5c59a781ff703dec21c7ee4010f31153144328c
diff --git a/sci-mathematics/rw/rw-0.8-r3.ebuild b/sci-mathematics/rw/rw-0.8-r3.ebuild
new file mode 100644
index 000000000000..6bbd3085010b
--- /dev/null
+++ b/sci-mathematics/rw/rw-0.8-r3.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Compute rank-width decompositions of graphs"
+HOMEPAGE="https://sourceforge.net/projects/rankwidth/"
+SRC_URI="https://downloads.sourceforge.net/project/rankwidth/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos"
+IUSE=""
+
+# We have a file collision (librw.so) with xpaint, bug 560210.
+RDEPEND="!media-gfx/xpaint"
+
+src_prepare() {
+ # The upstream tarball for v0.8 contains SYMLINKS to ar-lib,
+ # compile, install-sh, ltmain.sh, etc. And those symlinks don't
+ # always point to a working location for us, so we have to
+ # (re)generate actual files for that stuff. Bug 696986.
+ default
+ eautoreconf
+}
+
+src_configure() {
+ # The executable depends on igraph, which has gone off the rails
+ # upstream and has copy/pasted ~10 libraries into its src/ directory.
+ econf --disable-executable --disable-static
+}
+
+src_install() {
+ default
+
+ find "${ED}" -name '*.la' -delete \
+ || die 'failed to delete libtool archives'
+}
diff --git a/sci-mathematics/sympow/Manifest b/sci-mathematics/sympow/Manifest
new file mode 100644
index 000000000000..b97c2cec1e77
--- /dev/null
+++ b/sci-mathematics/sympow/Manifest
@@ -0,0 +1,5 @@
+AUX sympow-2.023.6-dont-force-O3.patch 2145 BLAKE2B 711d252e625690400ee7215f9f8d4e7c695945101d2114e18259d1c852795de9803f0b0866b37a6c99346ef3a398f45f6ee41fee949eb8aa8b5ae75042dc46d4 SHA512 6a60fb9f44867d2ba6aa33cfc34d6db7616da62a2d9c8a4ba1881459790c8760f162d0084b2d254938e8b5374fd929ca7f3a827312e76002587796ea516fbe6b
+AUX sympow-2.023.6-no-pkgdatafilesbindir-warnings.patch 2289 BLAKE2B 845125575e201767360ebe38ecbf321a254d01d5eadfeee4d36e7c350e939804d7726299d33de0c564f455b5a559c05542f0da5d54e6bcceb22c02907ec0599a SHA512 a5840039ff0bf6c99cd6ef5609bb46aeff48858a57a253e051a04b180839a0f8b36480fffee10e22ef76672073b08ca58a399cb078a477aa447bbbc0c05dd6cf
+DIST sympow-v2.023.6.tar.gz 68142 BLAKE2B accff25cb1da5b6935a91179fa399d76148709be54bbd434c0dc6143e88e9cd0f0a3cd96c683da3214366a29d6d0dbb7236d2623ef3f9322b6d4d54c6bad9882 SHA512 efe3b09fff0629e136b029ea615aa09ac1a4f225c06636d653ac921c7de01bf75e2b392a138c3c1af92f2b4f889f5949beeeba5b6e5e6b49e02c605bb9c16ceb
+EBUILD sympow-2.023.6.ebuild 1072 BLAKE2B 9862340cf5cc7262f660dec9eed43407ba0c3aa6642231677480983dc9d9b0ed6192023b7a3c92d4e849b8a43ec4640fd49726c0d266549695b640d682f61c69 SHA512 7b319c0994b88e87945c6bf535e13380dce1725070ebb3836e04076942bb26a24ca8b9e71fd534a8a08be6c9a8657c7fac0e2ce738b2f75ee90c2ca20b9f65ff
+MISC metadata.xml 740 BLAKE2B f7bf31eef4f6a42b64105e8ce1725e4792d5303d0adb524a23fb7286430449d15f4f2ecef1afa64bdb0b4e6941928aa75d081b8fdb0c3f7b679afdb7c71c2052 SHA512 45e110738e271c8b71325023e4e371dbaee1d9e7b7318d82dcc72b6e1d094799ab230e0a14d282a3a5badbe53c54f2ca44933c4acad5f1bd24798848ac663318
diff --git a/sci-mathematics/sympow/files/sympow-2.023.6-dont-force-O3.patch b/sci-mathematics/sympow/files/sympow-2.023.6-dont-force-O3.patch
new file mode 100644
index 000000000000..ae4924d468e3
--- /dev/null
+++ b/sci-mathematics/sympow/files/sympow-2.023.6-dont-force-O3.patch
@@ -0,0 +1,53 @@
+From d5fd3ce4221705c59dc289f14f5aefc2f974ba41 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Thu, 14 May 2020 18:45:59 -0400
+Subject: [PATCH 1/1] Configure: don't force -O3 in CFLAGS.
+
+The build system already respects the user's CFLAGS. It should respect
+lower -O levels as well. This is a "requirement" on Gentoo.
+---
+ Configure | 9 +++------
+ 1 file changed, 3 insertions(+), 6 deletions(-)
+
+diff --git a/Configure b/Configure
+index 1ef9756..fd5555c 100755
+--- a/Configure
++++ b/Configure
+@@ -104,15 +104,12 @@ CFLAGS=''
+ # return 2 if we did not add $FLAG.
+ try_add_CFLAG()
+ {
+- # We use -O3 here to really force generation of fused
+- # multiply-add instructions and to keep floats as much as
+- # possible in registers.
+ # We compile in the fpu.c which only does
+ # something if the macro x86 is defined.
+ local flag=$1 # first argument: C FLAG to test
+ local bypassfputest=${2:-nobypass} # second argument: whether or not bypass the numerical test (default: not)
+ local status=0
+- if $CC $ORIGINALCFLAGS -Werror $CFLAGS -O3 $flag config/fpubits1.c config/fpubits2.c fpu.c -o config/fpubits 2>/dev/null; then
++ if $CC $ORIGINALCFLAGS -Werror $CFLAGS $flag config/fpubits1.c config/fpubits2.c fpu.c -o config/fpubits 2>/dev/null; then
+ # Compiled successfully, now run it
+ config/fpubits >/dev/null 2>/dev/null
+ status=$?
+@@ -166,7 +163,7 @@ for FLAG in '' '-ffloat-store' '-O0'; do
+ done
+
+ # Check the actual FPU precision with our new flags.
+-CC_ARGS="$ORIGINALCFLAGS -O3 $CFLAGS config/fpubits1.c config/fpubits2.c fpu.c -o config/fpubits"
++CC_ARGS="$ORIGINALCFLAGS $CFLAGS config/fpubits1.c config/fpubits2.c fpu.c -o config/fpubits"
+ $CC $CC_ARGS
+ if [ $? -ne 0 ]; then
+ echo >&2 "Error: the command below failed:"
+@@ -256,7 +253,7 @@ echo "CONFEXE = config/endiantuple config/fpubits" >> $FILE
+ ##
+ ##echo "DEFS = $DEFS" >> $FILE
+
+-OPT="-O3 ${CFLAGS}" && echo "OPT = $OPT" >> $FILE
++OPT="${CFLAGS}" && echo "OPT = $OPT" >> $FILE
+
+ echo "H2MFLAGS = \\" >> $FILE
+ echo " --manual=\"SYMPOW package\" \\" >> $FILE
+--
+2.26.2
+
diff --git a/sci-mathematics/sympow/files/sympow-2.023.6-no-pkgdatafilesbindir-warnings.patch b/sci-mathematics/sympow/files/sympow-2.023.6-no-pkgdatafilesbindir-warnings.patch
new file mode 100644
index 000000000000..e3cbe823def7
--- /dev/null
+++ b/sci-mathematics/sympow/files/sympow-2.023.6-no-pkgdatafilesbindir-warnings.patch
@@ -0,0 +1,45 @@
+From cf182287eb4219b03e57352072449885e10543f3 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Fri, 15 May 2020 16:49:49 -0400
+Subject: [PATCH 1/1] main.c: hide pkgdatafilesbindir warnings behind VERBOSE
+ >= 2.
+
+The default "pkgdatafilesbindir" is something like /var/cache/sympow
+that will never be writable by unprivileged users (and cannot safely
+be made that way). There is already a fallback to $HOME in the code
+that works perfectly well, but by default sympow emits a warning when
+it realizes that it can't write to e.g. /var/cache/sympow on the first
+try. Since that's completely expected, we hide the warnings behind an
+additional level of verbosity (VERBOSE >= 2 instead of VERBOSE >= 1).
+---
+ main.c | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/main.c b/main.c
+index 1d018df..fecd7d1 100644
+--- a/main.c
++++ b/main.c
+@@ -136,17 +136,17 @@ static void prepare_main(char *argv0)
+ asprintf(&pkgdatafilesbindir,"%s/datafiles/"ENDIANTUPLE,pkgcachedir);
+ if (stat(pkgdatafilesbindir,&infodb)) {mode_t mask=umask(0);
+ if (mkdir(pkgdatafilesbindir,(S_IRWXU|S_IRWXG|S_IRWXO|S_ISVTX)))
+- {if (VERBOSE>=1) fprintf(stderr,"**WARNING** failed to create data bin package cache folder %s\n",pkgdatafilesbindir);
++ {if (VERBOSE>=2) fprintf(stderr,"**WARNING** failed to create data bin package cache folder %s\n",pkgdatafilesbindir);
+ free(pkgdatafilesbindir); pkgdatafilesbindir=NULL;}
+ else
+ {stat(pkgdatafilesbindir,&infodb); pkgdatamode= infodb.st_mode & ~MASK;}
+ umask(mask);}
+ else
+ {if (!S_ISDIR(infodb.st_mode))
+- {if (VERBOSE>=1) fprintf(stderr,"**WARNING** %s exists but is not a directory\n",pkgdatafilesbindir);
++ {if (VERBOSE>=2) fprintf(stderr,"**WARNING** %s exists but is not a directory\n",pkgdatafilesbindir);
+ free(pkgdatafilesbindir); pkgdatafilesbindir=NULL;}
+ else if (access(pkgdatafilesbindir,(R_OK|W_OK|X_OK)))
+- {if (VERBOSE>=1) fprintf(stderr,"**WARNING** %s yields insufficient permissions\n",pkgdatafilesbindir);
++ {if (VERBOSE>=2) fprintf(stderr,"**WARNING** %s yields insufficient permissions\n",pkgdatafilesbindir);
+ free(pkgdatafilesbindir); pkgdatafilesbindir=NULL;}
+ else {pkgdatamode= infodb.st_mode & ~MASK;}}
+ asprintf(&datafilesdir,"%s/datafiles",cachedir);
+--
+2.26.2
+
diff --git a/sci-mathematics/sympow/metadata.xml b/sci-mathematics/sympow/metadata.xml
new file mode 100644
index 000000000000..a321d1a8e2a3
--- /dev/null
+++ b/sci-mathematics/sympow/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mjo@gentoo.org</email>
+ </maintainer>
+ <!--
+ mjo: François maintained this package in the sage-on-gentoo overlay
+ long before I moved it into ::gentoo. You don't need an ACK from me
+ to merge his changes.
+ -->
+ <maintainer type="person">
+ <email>frp.bissey@gmail.com</email>
+ <name>François Bissey</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>proxy-maint@gentoo.org</email>
+ <name>Proxy Maintainers</name>
+ </maintainer>
+
+ <upstream>
+ <remote-id type="gitlab">rezozer/forks/sympow</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-mathematics/sympow/sympow-2.023.6.ebuild b/sci-mathematics/sympow/sympow-2.023.6.ebuild
new file mode 100644
index 000000000000..4e5e5566a81b
--- /dev/null
+++ b/sci-mathematics/sympow/sympow-2.023.6.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Symmetric power elliptic curve L-functions"
+HOMEPAGE="https://gitlab.com/rezozer/forks/sympow/"
+SRC_URI="https://gitlab.com/rezozer/forks/sympow/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="Sympow-BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# Pari is used at build time to generate data.
+BDEPEND="sys-apps/help2man
+ sci-mathematics/pari"
+DEPEND=""
+RDEPEND="sci-mathematics/pari"
+
+PATCHES=(
+ "${FILESDIR}/${P}-dont-force-O3.patch"
+ "${FILESDIR}/${P}-no-pkgdatafilesbindir-warnings.patch"
+)
+
+DOCS=( HISTORY README.md )
+
+src_configure() {
+ export ADDBINPATH=yes
+ export PREFIX="${EPREFIX}/usr"
+
+ # This location still won't be writable, but we can at least add
+ # the EPREFIX that belongs there. Sympow uses $HOME/.sympow as a
+ # fallback (what we want) when its first attempt doesn't work.
+ export VARPREFIX="${EPREFIX}/var"
+
+ ./Configure || die
+}
+
+src_compile() {
+ emake CC="$(tc-getCC)" all
+}
diff --git a/sci-mathematics/why3-for-spark/Manifest b/sci-mathematics/why3-for-spark/Manifest
index 11dcd5f5ea01..4b698d15808b 100644
--- a/sci-mathematics/why3-for-spark/Manifest
+++ b/sci-mathematics/why3-for-spark/Manifest
@@ -1,5 +1,5 @@
AUX why3-for-spark-2018-gentoo.patch 1015 BLAKE2B 201846ae0ef17bc6d777b7c1a8baddd1f684e82b811b16d2cce447423189a899f3e599cbf5cbd01630e2b246f8257ba5a890b20aaf62b0c1bc24e46642a37600 SHA512 871534c90f4f7c680f07dcd0bcacc4ce75c43b3132e8570b73e66316fe4333c244b9c443998916af7ff8fd297c20f7079ec5e8bf4c97207d0b7537722cd010a6
-AUX why3-for-spark-2019-gentoo.patch 432 BLAKE2B 44e4dda628cdd9b1d27d000ac0e9a37e56cb87a704cf7f83c634775f7ecf8d868d9750561e078c318be5079f91bf9e0f30de9616e781a8a128fdd853e74b431f SHA512 804d9914031450ebdeeea24d2aad472b1765e0534d8ebe404189f039d78be361b51deb21027c85f2d1919668c1f5ef25e65694424a22f7533e5cd264e7e5a191
+AUX why3-for-spark-2019-gentoo.patch 764 BLAKE2B ba9fd2c8ff6dfba4783c527cb02a5d40d0bc8d25e9039af20c1ae4498dfe7c275f5d3cf85a5bea63f86703dca8e931a4ce837c3fe4a2337918d87ec563d69de5 SHA512 61c2b1e8da73617211f9142738836be7787a9d2c2396fad73b6ed7f4d5bbe87336e38540549d8458d7ec2bd290cfdee811c4a6f19444b4e7b7de21396bcacef1
DIST why3-2019-20190517-197BB-src.tar.gz 9439414 BLAKE2B 68072064e8ee9152528c90afc948047a1f4d58b960ac05b276761fdca5ba1204100c75f33db7bb0ea1a8a646b734e62892ed41bd875b954354f52b8f9d498d4a SHA512 9169a4ff9ee994a19f9f04b689d1b9c679f5340bcd631d7d49b4c55064f505bd5a6ca8149077e5d24d36f5365f0cab58587094e86f352a9105fc46f10c0746ba
DIST why3-for-spark-gpl-2018-src.tar.gz 7682767 BLAKE2B 0b0272ca4d5519ca402990b234d0847378bcd2a0949fea78ea10e355233a16aebe79b938cdf8e4daadabb909171cab83b9d6ccacf9f2dc1c0b57bb6da6fd1fe0 SHA512 fc798acf343484fd8e70f470a318753c9a0e9967ff579f20ec185bf3c2a75e7a4a556388fc86a378610ce4a467f3e722c6f610da34d4c33bc3d6b10551731f07
EBUILD why3-for-spark-2018.ebuild 1712 BLAKE2B 6bab5512436341fe88e22657752081b5ed78f6ae27f1b3e5dc95a916a2b641f1f362aba40a333b74622a3832b5c385100d9266bdc25a692f43a20a93be2605a8 SHA512 0077d68c18911e71f5ff3a54b48700b3e63dbf976acf9f153ebb9ce81d8de6f697b9750be0ac5dfd214f40677a3dbe9325d8005df169a853b90980099d7ce762
diff --git a/sci-mathematics/why3-for-spark/files/why3-for-spark-2019-gentoo.patch b/sci-mathematics/why3-for-spark/files/why3-for-spark-2019-gentoo.patch
index f83a62566720..2dab12ddfbd3 100644
--- a/sci-mathematics/why3-for-spark/files/why3-for-spark-2019-gentoo.patch
+++ b/sci-mathematics/why3-for-spark/files/why3-for-spark-2019-gentoo.patch
@@ -12,3 +12,13 @@
let rec file_concat l =
match l with
+--- a/Makefile.in 2020-05-27 21:19:08.736241502 +0200
++++ b/Makefile.in 2020-05-27 21:19:14.042156954 +0200
+@@ -50,7 +50,6 @@
+ OCAMLINSTALLLIB = $(DESTDIR)@OCAMLINSTALLLIB@
+ OCAMLBEST = @OCAMLBEST@
+ OCAMLVERSION = @OCAMLVERSION@
+-CC = gcc
+ COQC = @COQC@
+ COQDEP = @COQDEP@
+ FRAMAC_LIBDIR = $(DESTDIR)@FRAMAC_LIBDIR@
diff --git a/sci-mathematics/wxmaxima/Manifest b/sci-mathematics/wxmaxima/Manifest
index db7256c68401..2414d502a250 100644
--- a/sci-mathematics/wxmaxima/Manifest
+++ b/sci-mathematics/wxmaxima/Manifest
@@ -2,8 +2,10 @@ DIST wxmaxima-18.11.4.tar.gz 12156776 BLAKE2B 75be0fb88402af011885616a646f7abcad
DIST wxmaxima-20.01.1.tar.gz 14011946 BLAKE2B ed80f02158aa0c43f37c040225010b35eea49756d8f052bcfa245d31a4a2203880463f51833ed40f2e1365473eb138269287c30a52e9f9b98ef4d9a5daac8cf5 SHA512 bff946f87db39b4bf416ef3440fdfea277f9dc9ed95debcea5798211299ae8c8dbb136a44be586a79e538b99fd38c46febf5378caab6ac31a01a01033f083937
DIST wxmaxima-20.01.3.tar.gz 14221966 BLAKE2B cdaf62f5456446fe6edf1247323faa9f0aeb84dbe890cb03028f9f441c4c6bd3e7acf806b71a86b156ea7f10664c0188517b8f2aa15536e3350e16e3307f412c SHA512 4a977bd293255ac3c010610c74aa39fba8b8468aaa9fc59707bab69ede7a427e261ce827bae8d302ee1343bb0fce5e7aa5ee3c59f17198d5c473637571667abd
DIST wxmaxima-20.02.4.tar.gz 15242422 BLAKE2B ea9dc613fa94d046a9d461c56a9d1564001f4fa28d90a553040e85b7dd442df025521dd9501257d12c808a2e9285b7f34b04c9f10d4ce658bc6d423055c9fbd7 SHA512 d5eb0e09de55c3e6ebafeaa95957ca8bbdacac9ec1d99f6041fa99b7fa59364b3228336675f9bffa71b879b17268b80c695f16c9259bee6d5cab9ef7ed86294b
+DIST wxmaxima-20.04.0.tar.gz 15313618 BLAKE2B 04a9544aeb1a7084250696fad99c51be21bf0b119581cebdf62b8dece3034ebcc1469b9d07576bfed8d72efe77ce6db47b5a29c4185a5e85114b552d3385caf9 SHA512 8caf9effa0167c3307eff4a6895a3b19b41aab37f845e4cdc139f3cdd03d9a061adc9ea4ad8ca7e0f28d83faf34d15f828f03c86d05ad7d83f0e28aee82aba70
EBUILD wxmaxima-18.11.4.ebuild 1324 BLAKE2B 1f6c20362bc7403da290ae6ae0bfa898b611d2986f770523d24780682562fa5c60a853697dda8507fe1ede01410b140bd6518cf1f5b0a65502fc36a9f0486a7d SHA512 e6102de11417007556f36485d8c37c100c0bc2f5df0cb39750ef5bda82d4c7a71d4036f7879e066dc407f45eab3e92122ae2c0494cbc94e607daf3982ea1702a
EBUILD wxmaxima-20.01.1.ebuild 1347 BLAKE2B d67dc143889163798e870e8ec3d04c3821bbb99ce4d1f114ecb5bc76756ae2b6fefba5b01e1ac45b16d6255dce909a9568eba1b1128dc89e127b1a329d4ac789 SHA512 7863680d2507d628741568a67954fa40962fbce8b78afdd83cf9f2612eae3d65e53a0a83b02f313b4a79e9acaf6094ac044a34c1cc6bca6ac7fa94df999c9a9b
EBUILD wxmaxima-20.01.3.ebuild 1347 BLAKE2B d67dc143889163798e870e8ec3d04c3821bbb99ce4d1f114ecb5bc76756ae2b6fefba5b01e1ac45b16d6255dce909a9568eba1b1128dc89e127b1a329d4ac789 SHA512 7863680d2507d628741568a67954fa40962fbce8b78afdd83cf9f2612eae3d65e53a0a83b02f313b4a79e9acaf6094ac044a34c1cc6bca6ac7fa94df999c9a9b
EBUILD wxmaxima-20.02.4.ebuild 1347 BLAKE2B d67dc143889163798e870e8ec3d04c3821bbb99ce4d1f114ecb5bc76756ae2b6fefba5b01e1ac45b16d6255dce909a9568eba1b1128dc89e127b1a329d4ac789 SHA512 7863680d2507d628741568a67954fa40962fbce8b78afdd83cf9f2612eae3d65e53a0a83b02f313b4a79e9acaf6094ac044a34c1cc6bca6ac7fa94df999c9a9b
+EBUILD wxmaxima-20.04.0.ebuild 1347 BLAKE2B d67dc143889163798e870e8ec3d04c3821bbb99ce4d1f114ecb5bc76756ae2b6fefba5b01e1ac45b16d6255dce909a9568eba1b1128dc89e127b1a329d4ac789 SHA512 7863680d2507d628741568a67954fa40962fbce8b78afdd83cf9f2612eae3d65e53a0a83b02f313b4a79e9acaf6094ac044a34c1cc6bca6ac7fa94df999c9a9b
MISC metadata.xml 711 BLAKE2B 00c54141e803d86fb20dc4f058fe99f6bbc2fd067175af6d0a5f893dc5a0b523fdd9116341ba33f991b11538989869337e1ce36c2259cfdb284725fed1aeaf60 SHA512 30a578958cbc4813e2615d0c3d7c4a1349f408933f285d3a43a382bf90bdf5c985ef1b844c4f8391205be643961de0335536ee800e1be24bf358bb4ead736fe5
diff --git a/sci-mathematics/wxmaxima/wxmaxima-20.04.0.ebuild b/sci-mathematics/wxmaxima/wxmaxima-20.04.0.ebuild
new file mode 100644
index 000000000000..9a2b704c52cf
--- /dev/null
+++ b/sci-mathematics/wxmaxima/wxmaxima-20.04.0.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+WX_GTK_VER="3.0"
+PLOCALES="ca cs da de el en es fi fr gl hu it ja kab nb pl pt_BR ru tr uk zh_CN zh_TW"
+inherit cmake-utils wxwidgets l10n xdg
+
+DESCRIPTION="Graphical frontend to Maxima, using the wxWidgets toolkit"
+HOMEPAGE="https://wxmaxima-developers.github.io/wxmaxima/"
+SRC_URI="https://github.com/wxMaxima-developers/wxmaxima/archive/Version-${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+S="${WORKDIR}"/${PN}-Version-${PV}
+
+DEPEND="
+ dev-libs/libxml2:2
+ x11-libs/wxGTK:${WX_GTK_VER}"
+RDEPEND="${DEPEND}
+ media-fonts/jsmath
+ sci-visualization/gnuplot[wxwidgets]
+ sci-mathematics/maxima"
+
+src_prepare() {
+ setup-wxwidgets
+ cmake-utils_src_prepare
+
+ sed -e "s|share/doc/${PN}|share/doc/${PF}|g" -i "${S}"/info/CMakeLists.txt \
+ || die "sed info/CMakeLists.txt failed"
+
+ # locales
+ rm_po() {
+ rm "${S}"/locales/wxMaxima/${1}.po || die "rm ${1}.po failed"
+ rm -f "${S}"/locales/manual/${1}.po
+ rm -f "${S}"/locales/wxwin/${1}.po
+ rm -f "${S}"/info/${PN}.${1}.md
+ rm -f "${S}"/info/${PN}.${1}.html
+ }
+ l10n_find_plocales_changes "${S}"/locales/wxMaxima '' '.po'
+ l10n_for_each_disabled_locale_do rm_po
+}
+
+src_install() {
+ docompress -x /usr/share/doc/${PF}
+ cmake-utils_src_install
+}