From f70601e0934acd62f6c5d06c5ede4cc607179514 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 7 Jul 2018 11:42:03 +0100 Subject: gentoo resync : 07.07.2018 --- sci-mathematics/Manifest.gz | Bin 14830 -> 14838 bytes sci-mathematics/octave/Manifest | 6 + .../files/octave-4.4.0-imagemagick-configure.patch | 16 ++ .../octave/files/octave-4.4.0-imagemagick.patch | 16 ++ .../octave/files/octave-4.4.0-qt-5.11.patch | 10 + .../octave/files/octave-4.4.0-texi.patch | 11 + sci-mathematics/octave/octave-4.4.0.ebuild | 195 ++++++++++++++++ sci-mathematics/rstudio/Manifest | 4 + .../files/rstudio-1.1.453-boost-1.67.0.patch | 38 ++++ .../rstudio/files/rstudio-1.1.453-core.patch | 143 ++++++++++++ sci-mathematics/rstudio/rstudio-1.1.453.ebuild | 250 +++++++++++++++++++++ 11 files changed, 689 insertions(+) create mode 100644 sci-mathematics/octave/files/octave-4.4.0-imagemagick-configure.patch create mode 100644 sci-mathematics/octave/files/octave-4.4.0-imagemagick.patch create mode 100644 sci-mathematics/octave/files/octave-4.4.0-qt-5.11.patch create mode 100644 sci-mathematics/octave/files/octave-4.4.0-texi.patch create mode 100644 sci-mathematics/octave/octave-4.4.0.ebuild create mode 100644 sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch create mode 100644 sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch create mode 100644 sci-mathematics/rstudio/rstudio-1.1.453.ebuild (limited to 'sci-mathematics') diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz index f86d63fa4ab0..f415cee47683 100644 Binary files a/sci-mathematics/Manifest.gz and b/sci-mathematics/Manifest.gz differ diff --git a/sci-mathematics/octave/Manifest b/sci-mathematics/octave/Manifest index 66ba8ee60f99..12466c114d0b 100644 --- a/sci-mathematics/octave/Manifest +++ b/sci-mathematics/octave/Manifest @@ -6,6 +6,12 @@ AUX octave-4.2.0-zlib-underlinking.patch 275 BLAKE2B a6353807c2c672b80ce5a015c56 AUX octave-4.2.2-fix-qscintilla-detection.patch 452 BLAKE2B bed48bf923cbfba50c50fdadfc807da0e199e2e7160f2a3078ba13fb58c123ecada0510ba8dd101f7772c7164533ff2aeb0841484ce41a86d27761b2e39e7fb0 SHA512 f5dd5a349dbdb36cba718ed378609f73090a32ce40240f002312539820538a30039c550c8b78493f3dca9e5f5eda8858c2e97afd313052d40d47d3edf08f1e80 AUX octave-4.2.2-imagemagick-configure.patch 873 BLAKE2B 9de92c88f83c56d521f83df7672e71bc9398ad782004339c737d2991d85154cc1cf2c3d5fe912892c87b18f51af6b11d4b8fadcc5ed058b76cfa604b93aaa720 SHA512 582df053f6c14790461408a180ce66589bd6501e3f9ecdc126b2cf12e8044198dff6eb66904b7704f87cba46adaabbac3126e46c61e406debe8cca49b935f93d AUX octave-4.2.2-ncurses-pkgconfig.patch 1034 BLAKE2B 244a96ab7cfd47203e7d23774c52f54e105f209edf79c869e6ce253a9cec7a3373a8dd0c98196ba3271f9b2b066ad3de3784151072055f2319ebbb4d1b68a475 SHA512 d2d6fe57a11f0493f86378bc4e1fc71378ae6d1878d17a367b77aa16a29880e37134e61343ba081f7ab2c4d127d93611491bef1320d6cd202eff0d78681cd4cc +AUX octave-4.4.0-imagemagick-configure.patch 862 BLAKE2B 46e5b0ab1f7e2fd261b012bebc7a21789df102f0467e93c72c02a0615dc05fce4def0dc26aabdd0d10922e51f53b93f57d15b71a983b0ebcb3c23a900f692c49 SHA512 17fe3cfdcfdde0caaedf7983f46f286cc7c66b39b7f696527cb8d217af7d9d63a4de26f798afb8a189b351c509c958ecfbab925f927449f97ae763fed750cd51 +AUX octave-4.4.0-imagemagick.patch 778 BLAKE2B 5f71ce6bc7ed9bc84f78f2bcb35d67232f0c550349f0212f653f49e837d7e28e3e87a0f47aca9629f9523c6972088d801270fe3d8e0c5bd487eac3db9cdb6b29 SHA512 dd111e621347c22de02829351fa6af4ea30e60ec5b3455a6bccce5e7794be93817651e607c81649f80511c7c1cc1a6a29ee27669af0660094a7f6ccdfdb8115d +AUX octave-4.4.0-qt-5.11.patch 346 BLAKE2B 0e9d5a2701ca789abaf9b396e5716226ce786fe259ae84ab8cbdeeff80dcf871945e1eec5260c14525744559ee8258e96ca5e8543ab21cff27ac21723078435f SHA512 48fbd44cf0af2ecc391c18a4fdd5e0f6682998f5ab5aadf5b2f1740504b4bd40fa24c08449c4ee50d47d0307748ff7fd5a23870e6b643658583260de8b338130 +AUX octave-4.4.0-texi.patch 570 BLAKE2B 83863f20e995eb4512944d6766b09a648b0d00b434f98f25db214ef6b3bcfa504d316dad984e7330ed51d972e5caec69c42797f703595a39d6acab7128270313 SHA512 e2d0390e586e001182a31a840ed6a93b4fb6ce0dd581f64460dcf3947783dd4755a8bd277f4babb6328f04cf653f02ac681952610d7eb70165936a9d79998c3f DIST octave-4.2.2.tar.gz 25624087 BLAKE2B c46de90d9a985c2b6b4f87b94b56f2ba4fb648ca0a0aff1f64e9b9d27a6d791e8657c2bff0c4daa3de5ac3622c23b34724e740ec1fe0f1a71d8f416c9f58d88a SHA512 b94edd79adc0e19229bb654037910201b51b6cfa373d63de5e3aa69e9b659b2e2790e2d2b4b5e8d2f12b26846c20ba5c12eae657155c8329e85e970f738d08c2 +DIST octave-4.4.0.tar.gz 29009355 BLAKE2B 3f7b4a6e1262cd0009f8649a570749acc2dc8b42aa1f88a6ce69b9c6bb99a95390f5a153c391a60ac118dc1e87f15596c7225764634c6076bb1ab3dfa4e09bcc SHA512 6a167a4a6a2f6ae70511f13b14feea0ce3efcc964227c93f3195adb3a1f1f28dda56f86a2e1c7c5e9f54891d2846fb96972092387e3da41f2e04cb700606ffc2 EBUILD octave-4.2.2.ebuild 5023 BLAKE2B 693ffa10fad508244db33ce1cd85d13a24653f119fae4562d279b3db0a81c6c47d5bff4cd8fd674f98479532ad952be95267333cc0b71e28bf5670763983f778 SHA512 d06c9fbe42c3bde1ef3df4c2d603968401faeb2c79503d775981ff8759007109853e7fe77c83797524276a38e64a6714b92e60735bfbb4cdc9202ced1401b759 +EBUILD octave-4.4.0.ebuild 5138 BLAKE2B 696f725740b8c752ac97c5abe396d6f002ff985c3cc59c0d6d7fd072ec1c1b022004eb1d025bd1a3c220ce719923e578746e02d374538ba2d8450175caefc1ba SHA512 601b5f650cf97d202018f4b07573953bfd2d9a1a6e4f4de474125b082174acb323e0e16c3b124e93c836846688cfae2342457385e4dd413ab834aeb68312f9ef MISC metadata.xml 1199 BLAKE2B f1daa0330bdc0362c68458ce6e7145118dd8a9d1a3bcbcc76c04ccdffe700c9d6f71b5e8b7f05b5ed0154352a213ce7b5177284919362585fedb0dbd8b68cbca SHA512 aebb1728f0ca59ba83b649eea72c267c530efc0b97b12f0d7958ba8de0f482fcb37245cf93bc188c9368686e0feafc44da4a7dd97d6bab8246309945fee8f7a4 diff --git a/sci-mathematics/octave/files/octave-4.4.0-imagemagick-configure.patch b/sci-mathematics/octave/files/octave-4.4.0-imagemagick-configure.patch new file mode 100644 index 000000000000..ce81b801d99c --- /dev/null +++ b/sci-mathematics/octave/files/octave-4.4.0-imagemagick-configure.patch @@ -0,0 +1,16 @@ +--- a/configure.ac 2018-04-30 19:03:56.000000000 +0200 ++++ a/configure.ac.new 2018-05-22 12:23:30.371174341 +0200 +@@ -1946,11 +1946,11 @@ + MAGICK_LIBS= + + PKG_CHECK_EXISTS([$magick++], [ +- dnl Make sure we only get -I, -L, and -l flags. ++ dnl Make sure we only get -I, -D, -L, and -l flags. + dnl Some Graphics/ImageMagick++ dnl packages add extra flags that are + dnl useful when building Graphics/ImageMagick++ extentions. These extra + dnl flags break the Octave build. +- MAGICK_CPPFLAGS="$($PKG_CONFIG --cflags-only-I $magick++ | $SED -e 's/^ *$//')" ++ MAGICK_CPPFLAGS=`$PKG_CONFIG --cflags $magick++ | sed -e 's/\(-@<:@DI@:>@@<:@^ \t@:>@*\)\|\(-@<:@^ \t@:>@*\)/\1/g'` + MAGICK_LDFLAGS="$($PKG_CONFIG --libs-only-L $magick++ | $SED -e 's/^ *$//')" + MAGICK_LIBS="$($PKG_CONFIG --libs-only-l $magick++ | $SED -e 's/^ *$//')" + diff --git a/sci-mathematics/octave/files/octave-4.4.0-imagemagick.patch b/sci-mathematics/octave/files/octave-4.4.0-imagemagick.patch new file mode 100644 index 000000000000..2f651e0995ee --- /dev/null +++ b/sci-mathematics/octave/files/octave-4.4.0-imagemagick.patch @@ -0,0 +1,16 @@ +--- a/libinterp/corefcn/__magick_read__.cc 2018-05-22 12:25:37.688173855 +0200 ++++ a/libinterp/corefcn/__magick_read__.cc.new 2018-05-22 12:32:51.475172200 +0200 +@@ -817,10 +817,11 @@ + // depth is 8, there's a good chance that we will be limited. It + // is also the GraphicsMagick recommended setting and the default + // for ImageMagick. +- if (QuantumDepth < 16) ++ using namespace Magick; ++ if (MAGICKCORE_QUANTUM_DEPTH < 16) + warning_with_id ("Octave:GraphicsMagick-Quantum-Depth", + "your version of %s limits images to %d bits per pixel\n", +- MagickPackageName, QuantumDepth); ++ MagickPackageName, MAGICKCORE_QUANTUM_DEPTH); + + initialized = true; + } diff --git a/sci-mathematics/octave/files/octave-4.4.0-qt-5.11.patch b/sci-mathematics/octave/files/octave-4.4.0-qt-5.11.patch new file mode 100644 index 000000000000..70ffbb471992 --- /dev/null +++ b/sci-mathematics/octave/files/octave-4.4.0-qt-5.11.patch @@ -0,0 +1,10 @@ +--- octave-4.4.0-orig/libgui/src/settings-dialog.cc 2018-05-01 03:03:56.000000000 +1000 ++++ octave-4.4.0/libgui/src/settings-dialog.cc 2018-07-03 19:35:41.865149269 +1000 +@@ -41,6 +41,7 @@ + #include + #include + #include ++#include + + #if defined (HAVE_QSCINTILLA) + # include "octave-qscintilla.h" diff --git a/sci-mathematics/octave/files/octave-4.4.0-texi.patch b/sci-mathematics/octave/files/octave-4.4.0-texi.patch new file mode 100644 index 000000000000..90ffa5361bf7 --- /dev/null +++ b/sci-mathematics/octave/files/octave-4.4.0-texi.patch @@ -0,0 +1,11 @@ +--- a/doc/interpreter/module.mk 2018-04-30 19:03:56.000000000 +0200 ++++ a/doc/interpreter/module.mk.new 2018-05-22 12:17:03.587175816 +0200 +@@ -368,6 +368,8 @@ + $(AWK) -f $(srcdir)/%reldir%/mkcontrib.awk $(srcdir)/%reldir%/contributors.in > $@-t && \ + mv $@-t $@ + ++%reldir%/preface.texi: %reldir%/contributors.texi ++ + AUTHORS: %reldir%/preface.texi %reldir%/contributors.texi | %reldir%/$(octave_dirstamp) + $(AM_V_MAKEINFO)rm -f $@-t $@ && \ + if [ "x$(srcdir)" != "x." ] && [ -f $(srcdir)/%reldir%/contributors.texi ] && [ ! -f %reldir%/contributors.texi ]; then \ diff --git a/sci-mathematics/octave/octave-4.4.0.ebuild b/sci-mathematics/octave/octave-4.4.0.ebuild new file mode 100644 index 000000000000..45ac0d9b327e --- /dev/null +++ b/sci-mathematics/octave/octave-4.4.0.ebuild @@ -0,0 +1,195 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools flag-o-matic fortran-2 gnome2-utils java-pkg-opt-2 pax-utils toolchain-funcs xdg-utils + +DESCRIPTION="High-level interactive language for numerical computations" +LICENSE="GPL-3" +HOMEPAGE="https://www.gnu.org/software/octave/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +SLOT="0/${PV}" +IUSE="curl doc fftw +glpk gnuplot graphicsmagick gui hdf5 +imagemagick java libressl opengl + portaudio postscript +qhull +qrupdate readline sndfile +sparse ssl static-libs X zlib" +KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux" + +RDEPEND=" + app-arch/bzip2 + app-text/ghostscript-gpl + dev-libs/libpcre:3= + sys-libs/ncurses:0= + sys-libs/zlib + virtual/blas + virtual/lapack + curl? ( net-misc/curl:0= ) + fftw? ( sci-libs/fftw:3.0= ) + glpk? ( sci-mathematics/glpk:0= ) + gnuplot? ( sci-visualization/gnuplot ) + gui? ( + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qthelp:5 + dev-qt/qtnetwork:5 + dev-qt/qtopengl:5 + dev-qt/qtprintsupport:5 + dev-qt/qtwidgets:5 + x11-libs/qscintilla:= + ) + hdf5? ( sci-libs/hdf5:0= ) + imagemagick? ( + !graphicsmagick? ( media-gfx/imagemagick:=[cxx] ) + graphicsmagick? ( media-gfx/graphicsmagick:=[cxx] ) + ) + java? ( >=virtual/jre-1.6.0:* ) + opengl? ( + media-libs/freetype:2= + media-libs/fontconfig:1.0= + virtual/glu + >=x11-libs/fltk-1.3:1=[opengl,xft] + x11-libs/gl2ps:0= + ) + ssl? ( + !libressl? ( dev-libs/openssl:0= ) + libressl? ( dev-libs/libressl:0= ) + ) + portaudio? ( media-libs/portaudio ) + postscript? ( + app-text/epstool + media-gfx/pstoedit + media-gfx/transfig + ) + qhull? ( media-libs/qhull:0= ) + qrupdate? ( sci-libs/qrupdate:0= ) + readline? ( sys-libs/readline:0= ) + sndfile? ( media-libs/libsndfile ) + sparse? ( + sci-libs/arpack:0= + sci-libs/camd:0= + sci-libs/ccolamd:0= + sci-libs/cholmod:0= + sci-libs/colamd:0= + sci-libs/cxsparse:0= + sci-libs/umfpack:0= + ) + X? ( x11-libs/libX11:0= )" +DEPEND="${RDEPEND} + dev-util/gperf + sys-apps/texinfo + virtual/pkgconfig + doc? ( + dev-texlive/texlive-fontsrecommended + || ( dev-texlive/texlive-plaingeneric dev-texlive/texlive-genericrecommended ) + dev-texlive/texlive-metapost + virtual/latex-base + ) + gui? ( dev-qt/linguist-tools:5 ) + java? ( >=virtual/jdk-1.6.0 ) + qrupdate? ( app-misc/pax-utils ) + sparse? ( app-misc/pax-utils )" + +PATCHES=( + "${FILESDIR}"/${PN}-4.4.0-texi.patch + "${FILESDIR}"/${PN}-4.2.0-disable-getcwd-path-max-test-as-it-is-too-slow.patch + "${FILESDIR}"/${PN}-4.4.0-imagemagick-configure.patch + "${FILESDIR}"/${PN}-4.4.0-imagemagick.patch + "${FILESDIR}"/${PN}-4.2.0-pkgbuilddir.patch + "${FILESDIR}"/${PN}-4.2.2-ncurses-pkgconfig.patch + "${FILESDIR}"/${PN}-4.2.0-zlib-underlinking.patch + "${FILESDIR}"/${PN}-4.4.0-qt-5.11.patch +) + +src_prepare() { + # nasty prefix hacks for fltk:1 linking + if use prefix; then + use opengl && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/fltk-1" + fi + + # occasional fail on install, force regeneration (bug #401189) + rm doc/interpreter/contributors.texi || die + + default + eautoreconf +} + +src_configure() { + # [QA] detect underlinking #593670 + append-ldflags $(test-flags-CXX -Wl,-z,defs) + + # unfortunate dependency on mpi from hdf5 (bug #302621) + use hdf5 && has_version sci-libs/hdf5[mpi] && \ + export CXX=mpicxx CC=mpicc FC=mpif77 F77=mpif77 + + econf \ + --localstatedir="${EPREFIX}/var/state/octave" \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ + --disable-64 \ + --disable-jit \ + --enable-shared \ + --with-z \ + --with-bz2 \ + --without-OSMesa \ + $(use_enable static-libs static) \ + $(use_enable doc docs) \ + $(use_enable java) \ + $(use_enable readline) \ + $(use_with curl) \ + $(use_with fftw fftw3) \ + $(use_with fftw fftw3f) \ + $(use_enable fftw fftw-threads) \ + $(use_with glpk) \ + $(use_with hdf5) \ + $(use_with imagemagick magick $(usex graphicsmagick GraphicsMagick ImageMagick)) \ + $(use_with opengl) \ + $(use_with opengl fltk) \ + $(use_with ssl openssl) \ + $(use_with portaudio) \ + $(use_with qhull) \ + $(use_with qrupdate) \ + $(use_with gui qt 5) \ + $(use_with sndfile) \ + $(use_with sparse arpack) \ + $(use_with sparse umfpack) \ + $(use_with sparse colamd) \ + $(use_with sparse ccolamd) \ + $(use_with sparse cholmod) \ + $(use_with sparse cxsparse) \ + $(use_with X x) +} + +src_compile() { + default + if use java; then + pax-mark m "${S}/src/.libs/octave-cli" + fi +} + +src_install() { + default + if use doc; then + dodoc $(find doc -name '*.pdf') + else + # bug 566134, macros.texi is installed by make install if use doc + insinto /usr/share/${PN}/${PV}/etc + doins doc/interpreter/macros.texi + fi + [[ -e test/fntests.log ]] && dodoc test/fntests.log + use java && \ + java-pkg_regjar "${ED%/}/usr/share/${PN}/${PV}/m/java/octave.jar" + echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}/${PV}" > 99octave || die + doenvd 99octave +} + +pkg_postinst() { + gnome2_icon_cache_update + xdg_mimeinfo_database_update + xdg_desktop_database_update +} + +pkg_postrm() { + gnome2_icon_cache_update + xdg_mimeinfo_database_update + xdg_desktop_database_update +} diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest index 7d3b5d3ae0fb..5be238bfddb2 100644 --- a/sci-mathematics/rstudio/Manifest +++ b/sci-mathematics/rstudio/Manifest @@ -5,6 +5,8 @@ AUX rstudio-0.99.879-prefs.patch 1859 BLAKE2B f324ab7b87e7cef32ac8b2718059200e40 AUX rstudio-1.0.44-paths.patch 6722 BLAKE2B 46351eb6eda15f74b03f1c5beb0b22bb835f4312af1889997e042657383a0130986bf4ecbc45dac98aafed7c317048e8bb380287a79be696c5c0a403e5633857 SHA512 6191520733f33466cf45bcc102a386763acc37a0cc1c58718cb59f3e3b5549afe5a051039f50aa390d773433d992cdff11bdf27c7e2960eb6177cd99c3169828 AUX rstudio-1.0.44-systemd.patch 1147 BLAKE2B ca1b24c2544ff2cb6b9e7a91b4ce25eda7f034a6bff91c2495a993e8ab69062a839f85f4ecb2604bbada7df40e67ab5476fdf05c5ebf48d1518dd7f1b950aae7 SHA512 ee22d4421ab52cff1815200ce1bda33ba7af752363537c6875ea19151767722183861301082eb03cb34403a08981cb10d66fd496e9e2687a4f3ca9de98f33d91 AUX rstudio-1.1.357-clang-pandoc.patch 3240 BLAKE2B bc7f55d2f2cea64643d02af314afbbd0df1d986889d0d3a2bbf6878e9f8ec7d73710c7e631bf0cbf04b4ecf4142236ef7a1dc0a073d34958a8bd0828594f605d SHA512 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eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade DIST rstudio-1.1.383.tar.gz 20196702 BLAKE2B 5164230a92618e4252269ad0016b200294d1e7fa502cc49aa694486cda098ee7ffc65e6c74a87d891d0532f5cc15d1552aa86d04047d07b4f275cbc4d2758647 SHA512 3f637f9bce2c1ad1a4ed3e74287da722190a4e12b0cace6ffcca271977d49dcecca9365f2064366aad94e87851593cab83fa9361e9a9222a9f67fe9451f31ed2 +DIST rstudio-1.1.453.tar.gz 20200360 BLAKE2B 560b89e53b04356ecf9a02dd8a7e72ad8d6c30bf406fbe7e22a82cc6d33d40e84bececf5ecda9cf086360b2bd2fa64d6b33c2dd675ef5f605f9e825d7ca2dc84 SHA512 f2be0866f645007a6f80959109928820c89480057c3660d23e790591797d4f4c371733f49290dae9c81bfc2715821528e2a105e7a66d4d9ffbfc7ee2a596976c 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-1.1.383-r1.ebuild 8339 BLAKE2B d6dd6efec40207a2a042827dffa99eb3bf9c820e385ee22dbe89ec0dabe60af523da054a8492ee97164eb4a2da47f3cb8848637a5d858111200767c2f689e53a SHA512 05cff959e87bf90125935b130544ae6d1ea4283069bae3d55f415037f97e44ca1ae032d595701157abd9d49d106e77bb8fd42085fa8a9167e7ff5ed981dcf86c +EBUILD rstudio-1.1.453.ebuild 8504 BLAKE2B ecf0e0da004695e5b5520801c4cb3954b4498b9bf2ac651b78ab4cfd82f1228a4fa92b70350ce72c0b36cb311e5cee8fe5026850262d78c51385022803b8429e SHA512 003a9ac1cbefe121d79e70d6a618ac67aee7b83d38ec94ef11f79c70caf10e0c4e312cf13958fd28649ab065939a8c3e8345c30d9e84638e84e3bd5e28b9e193 MISC metadata.xml 590 BLAKE2B 53dc62775e118c9c26ee05e20ee1da1ac31b6a6b74cf7dac410856fe4e0cce40fbb800c7a03e60f59e14442baf3aad866ad42616ad5fbb5724f7f6d8c1636eea SHA512 7111442aaa52da1e554c34f824113ec0e227798dd11b0ea9148b81e7a31c08b2a527b9995e3adb9363c7a4f2a8594f30cbd4a179545bf31d69f07d5558c20f52 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 new file mode 100644 index 000000000000..760c9b561055 --- /dev/null +++ b/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch @@ -0,0 +1,38 @@ +--- 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(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(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(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(kDefaultTimeoutInterval)); ++boost::posix_time::seconds FileLock::s_refreshRate(static_cast(kDefaultRefreshRate)); + bool FileLock::s_loggingEnabled(false); + bool FileLock::s_isLoadBalanced(false); + FilePath FileLock::s_logFile; diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch new file mode 100644 index 000000000000..641f7710167a --- /dev/null +++ b/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch @@ -0,0 +1,143 @@ +--- 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 @@ + } + + // prepare session info +- json::Object sessionInfo ; ++ core::json::Object sessionInfo ; + sessionInfo["clientId"] = clientId; + sessionInfo["mode"] = options.programMode(); + +@@ -119,8 +119,8 @@ + } + + // temp dir +- FilePath tempDir = rstudio::r::session::utils::tempDir(); +- Error error = tempDir.ensureDirectory(); ++ core::FilePath tempDir = rstudio::r::session::utils::tempDir(); ++ core::Error error = tempDir.ensureDirectory(); + if (error) + LOG_ERROR(error); + sessionInfo["temp_dir"] = tempDir.absolutePath(); +@@ -132,12 +132,12 @@ + sessionInfo["prompt"] = rstudio::r::options::getOption("prompt"); + + // client state +- json::Object clientStateObject; ++ core::json::Object clientStateObject; + rstudio::r::session::clientState().currentState(&clientStateObject); + sessionInfo["client_state"] = clientStateObject; + + // source documents +- json::Array jsonDocs; ++ core::json::Array jsonDocs; + error = modules::source::clientInitDocuments(&jsonDocs); + if (error) + LOG_ERROR(error); +@@ -159,7 +159,7 @@ + if (resumed) + { + // console actions +- json::Object actionsObject; ++ core::json::Object actionsObject; + consoleActions.asJson(&actionsObject); + sessionInfo["console_actions"] = actionsObject; + } +@@ -211,12 +211,12 @@ + } + else + { +- sessionInfo["active_project_file"] = json::Value(); +- sessionInfo["project_ui_prefs"] = json::Value(); +- sessionInfo["project_open_docs"] = json::Value(); ++ sessionInfo["active_project_file"] = core::json::Value(); ++ sessionInfo["project_ui_prefs"] = core::json::Value(); ++ sessionInfo["project_open_docs"] = core::json::Value(); + sessionInfo["project_supports_sharing"] = false; + sessionInfo["project_owned_by_user"] = false; +- sessionInfo["project_user_data_directory"] = json::Value(); ++ sessionInfo["project_user_data_directory"] = core::json::Value(); + } + + sessionInfo["system_encoding"] = std::string(::locale2charset(NULL)); +@@ -253,20 +253,20 @@ + sessionInfo["build_tools_bookdown_website"] = + module_context::isBookdownWebsite(); + +- FilePath buildTargetDir = projects::projectContext().buildTargetPath(); ++ core::FilePath buildTargetDir = projects::projectContext().buildTargetPath(); + if (!buildTargetDir.empty()) + { + sessionInfo["build_target_dir"] = module_context::createAliasedPath( + buildTargetDir); +- sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) && ++ sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) && + buildTargetDir.childPath("src").exists(); + sessionInfo["has_pkg_vig"] = +- (type == r_util::kBuildTypePackage) && ++ (type == core::r_util::kBuildTypePackage) && + buildTargetDir.childPath("vignettes").exists(); + } + else + { +- sessionInfo["build_target_dir"] = json::Value(); ++ sessionInfo["build_target_dir"] = core::json::Value(); + sessionInfo["has_pkg_src"] = false; + sessionInfo["has_pkg_vig"] = false; + } +@@ -274,9 +274,9 @@ + } + else + { +- sessionInfo["build_tools_type"] = r_util::kBuildTypeNone; ++ sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone; + sessionInfo["build_tools_bookdown_website"] = false; +- sessionInfo["build_target_dir"] = json::Value(); ++ sessionInfo["build_target_dir"] = core::json::Value(); + sessionInfo["has_pkg_src"] = false; + sessionInfo["has_pkg_vig"] = false; + } +@@ -285,7 +285,7 @@ + sessionInfo["presentation_commands"] = options.allowPresentationCommands(); + + sessionInfo["tutorial_api_available"] = false; +- sessionInfo["tutorial_api_client_origin"] = json::Value(); ++ sessionInfo["tutorial_api_client_origin"] = core::json::Value(); + + sessionInfo["build_state"] = modules::build::buildStateAsJson(); + sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled(); +@@ -296,7 +296,7 @@ + + // console history -- we do this at the end because + // restoreBuildRestartContext may have reset it +- json::Array historyArray; ++ core::json::Array historyArray; + rstudio::r::session::consoleHistory().asJson(&historyArray); + sessionInfo["console_history"] = historyArray; + sessionInfo["console_history_capacity"] = +@@ -364,13 +364,13 @@ + + sessionInfo["multi_session"] = options.multiSession(); + +- json::Object rVersionsJson; ++ core::json::Object rVersionsJson; + rVersionsJson["r_version"] = module_context::rVersion(); + rVersionsJson["r_home_dir"] = module_context::rHomeDir(); + sessionInfo["r_versions_info"] = rVersionsJson; + + sessionInfo["show_user_home_page"] = options.showUserHomePage(); +- sessionInfo["user_home_page_url"] = json::Value(); ++ sessionInfo["user_home_page_url"] = core::json::Value(); + + sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson(); + sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload(); +@@ -394,7 +394,7 @@ + + // send response (we always set kEventsPending to false so that the client + // won't poll for events until it is ready) +- json::JsonRpcResponse jsonRpcResponse ; ++ core::json::JsonRpcResponse jsonRpcResponse ; + jsonRpcResponse.setField(kEventsPending, "false"); + jsonRpcResponse.setResult(sessionInfo) ; + ptrConnection->sendJsonRpcResponse(jsonRpcResponse); diff --git a/sci-mathematics/rstudio/rstudio-1.1.453.ebuild b/sci-mathematics/rstudio/rstudio-1.1.453.ebuild new file mode 100644 index 000000000000..b69961db0c96 --- /dev/null +++ b/sci-mathematics/rstudio/rstudio-1.1.453.ebuild @@ -0,0 +1,250 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils + +# TODO +# * package gin and gwt +# * use dict from tree, linguas +# * do src_test (use junit from tree?) + +# update from scripts in dependencies/common +# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt +GWT_VER=2.7.0 +GIN_VER=1.5 +SELENIUM_VER=2.37.0 +CHROMEDRIVER_VER=2.7 +# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc +PANDOC_VER=1.19.2.1 +# ls dependencies/common/*.tar.gz +PACKRAT_VER=0.98.1000 +RMARKDOWN_VER=0.98.1000 +SHINYAPPS_VER=0.98.1000 +RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0 + +DESCRIPTION="IDE for the R language" +HOMEPAGE=" + http://www.rstudio.org + https://github.com/rstudio/rstudio/" +SRC_URI=" + https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip + https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip + https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip + https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar + https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux + https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip + https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz + https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz + https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz + https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz +" + +LICENSE="AGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="dedicated libressl server" + +QT_VER=5.4 +QT_SLOT=5 +RDEPEND=" + >=app-text/pandoc-${PANDOC_VER} + dev-haskell/pandoc-citeproc + >=dev-lang/R-2.11.1 + >=dev-libs/boost-1.63:= + >=dev-libs/mathjax-2.7.4 + sys-apps/util-linux + >=sys-devel/clang-3.5.0:* + sys-libs/zlib + >=virtual/jre-1.8:= + x11-libs/pango + !dedicated? ( + >=dev-qt/qtcore-${QT_VER}:${QT_SLOT} + >=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT} + >=dev-qt/qtdbus-${QT_VER}:${QT_SLOT} + >=dev-qt/qtgui-${QT_VER}:${QT_SLOT} + >=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT} + >=dev-qt/qtopengl-${QT_VER}:${QT_SLOT} + >=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT} + >=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT} + >=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)] + >=dev-qt/qtsensors-${QT_VER}:${QT_SLOT} + >=dev-qt/qtsql-${QT_VER}:${QT_SLOT} + >=dev-qt/qtsvg-${QT_VER}:${QT_SLOT} + >=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT} + >=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT} + >=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT} + >=dev-qt/qtxml-${QT_VER}:${QT_SLOT} + >=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT} + server? ( virtual/pam ) + ) + dedicated? ( virtual/pam ) + !libressl? ( dev-libs/openssl:0 ) + libressl? ( dev-libs/libressl:0 )" +DEPEND="${RDEPEND} + app-arch/unzip + dev-java/ant-core + >=virtual/jdk-1.8:= + virtual/pkgconfig" +# test? ( dev-java/junit:4 ) + +PATCHES=( + "${FILESDIR}/${PN}-0.99.879-prefs.patch" + "${FILESDIR}/${PN}-1.0.44-paths.patch" + "${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch" + "${FILESDIR}/${PN}-0.98.490-linker_flags.patch" + "${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch" + "${FILESDIR}/${PN}-1.0.44-systemd.patch" + "${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch" + "${FILESDIR}/${PN}-1.1.453-core.patch" +) + +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=$(get_version_component_range 1) + export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2) + export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3) + + local mycmakeargs=( + -DDISTRO_SHARE=share/${PN} + -DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")" + -DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")") + -DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake + -DRSTUDIO_VERIFY_R_VERSION=FALSE + ) + + cmake-utils_src_configure +} + +src_compile() { + # Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny + # P: /root/.oracle_jre_usage. + export ANT_OPTS="-Duser.home=${T}" + cmake-utils_src_compile +} + +src_install() { + export ANT_OPTS="-Duser.home=${T}" + cmake-utils_src_install + pax-mark m "${ED}usr/bin/rstudio" + doconfd "${FILESDIR}"/rstudio-server.conf + dodir /etc/rstudio + insinto /etc/rstudio + doins "${FILESDIR}"/rsession.conf + dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}etc/rstudio/rserver.conf" + if use dedicated || use server; then + dopamd src/cpp/server/extras/pam/rstudio + newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server + fi +} + +pkg_preinst() { + use dedicated || gnome2_icon_savelist + java-pkg-2_pkg_preinst +} + +pkg_postinst() { + use dedicated || { xdg_desktop_database_update + xdg_mimeinfo_database_update + gnome2_icon_cache_update ;} + + if use dedicated || use server; then + enewgroup rstudio-server + enewuser rstudio-server -1 -1 -1 rstudio-server + fi +} + +pkg_postrm() { + use dedicated || { xdg_desktop_database_update + xdg_mimeinfo_database_update + gnome2_icon_cache_update ;} +} -- cgit v1.2.3