From 8935c90a52d77191e71f2211d16f0d301c99e16b Mon Sep 17 00:00:00 2001 From: Denis Dupeyron Date: Mon, 5 Mar 2012 17:23:05 +0000 Subject: Version bump. Add patches to fix handling of library writability and package updates. Package-Manager: portage-2.1.10.49/cvs/Linux x86_64 --- dev-lang/R/ChangeLog | 10 +- dev-lang/R/Manifest | 18 +-- dev-lang/R/R-2.14.2.ebuild | 159 +++++++++++++++++++++ .../R/files/R-2.14.2-library-writability.patch | 40 ++++++ .../R/files/R-2.14.2-prune-package-update.patch | 25 ++++ dev-lang/R/metadata.xml | 8 +- 6 files changed, 245 insertions(+), 15 deletions(-) create mode 100644 dev-lang/R/R-2.14.2.ebuild create mode 100644 dev-lang/R/files/R-2.14.2-library-writability.patch create mode 100644 dev-lang/R/files/R-2.14.2-prune-package-update.patch (limited to 'dev-lang/R') diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog index 43fccc72ab44..0db08c2f0f33 100644 --- a/dev-lang/R/ChangeLog +++ b/dev-lang/R/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for dev-lang/R # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.195 2012/02/27 02:55:58 bicatali Exp $ +# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.196 2012/03/05 17:23:05 calchan Exp $ + +*R-2.14.2 (05 Mar 2012) + + 05 Mar 2012; Denis Dupeyron +R-2.14.2.ebuild, + +files/R-2.14.2-library-writability.patch, + +files/R-2.14.2-prune-package-update.patch, metadata.xml: + Version bump. Add patches to fix handling of library writability and package + updates. 27 Feb 2012; Sébastien Fabbro R-2.14.1.ebuild, +files/R-2.14.1-warnings-buffer-overflow.patch: diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index ae72e7cc8e46..f4de257a98dc 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,6 +1,3 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX R-2.11.1-parallel.patch 633 RMD160 e2ba77a67870123faac6c62e454492d4ee70ad92 SHA1 6fec3a4dce03a64daf4f59ca1bbfe828adc83ae2 SHA256 4ad6f007ffb390584de0c8a5935e98f98106f32394aac45c30c3fdfe77c00c70 AUX R-2.12.1-ldflags.patch 639 RMD160 ce9052b344ca706608495c54e5d338b627060b83 SHA1 cada00c963e75458c9d145b07a3378a20e221f82 SHA256 dee11fd510d31add8166230a7af61b7e700f2f4f122cbe0a07310d0017874933 AUX R-2.13.1-zlib_header_fix.patch 464 RMD160 908fd31070ac6e3311ad4105763a7b89f5d1d446 SHA1 a261faef7bd39de543952d0d9676319bf310a0b5 SHA256 161f0fff63db5cb2cb4894321759997e75463d784d5a7ba5105f74fe2ed73c40 @@ -8,17 +5,14 @@ AUX R-2.14.1-pcre830.patch 949 RMD160 45dfda7325392d88c7b3b382db3cd29a188c3d7c S AUX R-2.14.1-rmath-shared.patch 986 RMD160 ec0adb2b8c8d8932eedebda776cf204e3c7ea01e SHA1 a837510d2f154cf33ba1f70272a0bb10266c9b3f SHA256 c05463dbf9ec5bba34cc987df4f6878154a738e57aaeaac46cc4f728c0c837a7 AUX R-2.14.1-tiff.patch 1711 RMD160 cb6b5b2c160011c7dfebabc0f4bcae5a5ab03a90 SHA1 0b2b5cbd3cfef9eee1968ff7dab2c8fca051e9d4 SHA256 ff77e062a80eeb403dc98ffb0b6fedce28859f18082981891ae6e2a95cf61142 AUX R-2.14.1-warnings-buffer-overflow.patch 380 RMD160 acf41913d9eda01ebbb7c077edf9bf1bbb47c3ae SHA1 bb6fc5b8216b1ccfed7e37fc57870215016676c5 SHA256 e6b3e825ef837342c0a4bbfc05d7441d1ec5a98e31cf3bdb3d25000337a8538f +AUX R-2.14.2-library-writability.patch 2042 RMD160 ffee246fc02e18fe9c091822593973802868d4b4 SHA1 222670e47a0e590b9dda72822ae1c81731f9fc88 SHA256 7bb20306c7cec885c219b7eedbf27b38b14bd30e752139a4eba14fdac5515d9d +AUX R-2.14.2-prune-package-update.patch 1173 RMD160 1d735be7298eab1f0ff019019e94a1d6aca14810 SHA1 2eeb4ff5ccf336b701842474f6a9071ef762fb19 SHA256 386c382daf23199a620e6c6d73a4be1a17e611d1ff08c82aeb7c51a9ebe02314 DIST R-2.10.1.tar.gz 19705604 RMD160 7acf060192f205da4731d0ea3c2cc318b65b7e91 SHA1 f5b1969fde3642c233f5198e44a7bf17a7b85ab6 SHA256 5ca1780d9f47f2f4a9b52ba44fed9ee6e7d3547f18ed2c05192b0dbc56038e9d DIST R-2.14.1.tar.gz 23697861 RMD160 9dcd1d135701e3c682585346e7c48ac2c62012fd SHA1 5803a213480a749e36bccc155aecb13070ade096 SHA256 d8a18914005975f40ed8fb37e3532422f769fb454651a9ed75f73c2bee9c0c4c +DIST R-2.14.2.tar.gz 23893986 RMD160 6055dd28a99baa7b23c55f74dc1479e93a0dee58 SHA1 523dca7694e4d0c8701fcc783ea3767e46fe7a62 SHA256 ccd8b43a746dc7105a1c77423ea1bb72dc333b41d9e9801a96d6f71c2266736e DIST R.bash_completion.bz2 4019 RMD160 796951fb32e9ea4074dcd5ba3da5955ec0193993 SHA1 05ddebef0df16f0bf35aecc8fcb702ad5d106e5e SHA256 424790f7be27a0aad7b65289c97cb15d2ca9ee272f30f3e5c906217e487c7f85 EBUILD R-2.10.1.ebuild 4514 RMD160 7f170bfc025de21298d01f6b44ac3714605146fd SHA1 2a4d80e1e2ab22e2b3bfa2e910770185b81ee584 SHA256 86e6ab59bf58155d0dc313ecc3a07281b471074b3a178058c96fa8e4e3e3dea8 EBUILD R-2.14.1.ebuild 4327 RMD160 ff7b567055bdb11dc8ba276f50a0486cebda9910 SHA1 f23735533c94b4435c5f3dfebe2b729ab5a72be9 SHA256 015dca3585c42f807f0907c7f6e1809123d79055c13cd4d3e83e5d02c17bb8ba -MISC ChangeLog 29432 RMD160 cbb8bb79f780cfce02a7698acff0909ee62fb14e SHA1 2b0b6d74c49ba9439ca7baff39a648f85f73d052 SHA256 06bfe1a764e30e96c9b0aa3c560abe5b91b502a6fdf8cff8d2999ec959478982 -MISC metadata.xml 1033 RMD160 d200586401de4f212758a5632040059b86cebe79 SHA1 7e6e9da0f5fe1f39a440ecdb298775685f14bb31 SHA256 c0e2a21f7e4e5eeadfd2502b7d035633b81a8f0228e4986758fb0f45990ec016 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.18 (GNU/Linux) - 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( mirror://gentoo/R.bash_completion.bz2 )" + +LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd" +IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png profile readline static-libs tiff tk X" +REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" + +CDEPEND="app-arch/bzip2 + app-text/ghostscript-gpl + dev-libs/libpcre + virtual/blas + virtual/fortran + cairo? ( x11-libs/cairo[X] x11-libs/pango ) + icu? ( dev-libs/icu ) + jpeg? ( virtual/jpeg ) + lapack? ( virtual/lapack ) + perl? ( dev-lang/perl ) + png? ( media-libs/libpng ) + readline? ( sys-libs/readline ) + tk? ( dev-lang/tk ) + X? ( x11-libs/libXmu x11-misc/xdg-utils )" + +DEPEND="${CDEPEND} + dev-util/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + )" + +RDEPEND="${CDEPEND} + ( || ( =sys-libs/zlib-1.2.5.1-r2[minizip] ) ) + app-arch/xz-utils + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test )" + +R_DIR="${EPREFIX}/usr/$(get_libdir)/${PN}" + +pkg_setup() { + if use openmp; then + FORTRAN_NEED_OPENMP=1 + tc-has-openmp || die "Please enable openmp support in your compiler" + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-2.11.1-parallel.patch \ + "${FILESDIR}"/${PN}-2.12.1-ldflags.patch \ + "${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch \ + "${FILESDIR}"/${PN}-2.14.1-tiff.patch \ + "${FILESDIR}"/${PN}-2.14.1-rmath-shared.patch \ + "${FILESDIR}"/${PN}-2.14.1-warnings-buffer-overflow.patch \ + "${FILESDIR}"/${PN}-2.14.2-library-writability.patch \ + "${FILESDIR}"/${PN}-2.14.2-prune-package-update.patch + + # fix packages.html for doc (bug #205103) + sed -i \ + -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ + src/library/tools/R/Rd.R || die + + # fix Rscript path when installed (bug #221061) + sed -i \ + -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${R_DIR}\"':" \ + src/unix/Makefile.in || die "sed unix Makefile failed" + + # fix HTML links to manual (bug #273957) + sed -i \ + -e 's:\.\./manual/:manual/:g' \ + $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use lapack && \ + export LAPACK_LIBS="$(pkg-config --libs lapack)" + + if use X; then + export R_BROWSER="$(type -p xdg-open)" + export R_PDFVIEWER="$(type -p xdg-open)" + fi + use perl && \ + export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}" + AT_M4DIR=m4 eaclocal + eautoconf +} + +src_configure() { + econf \ + --enable-byte-compiled-packages \ + --enable-R-shlib \ + --with-system-zlib \ + --with-system-bzlib \ + --with-system-pcre \ + --with-system-xz \ + --with-blas="$(pkg-config --libs blas)" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable nls) \ + $(use_enable openmp) \ + $(use_enable profile R-profiling) \ + $(use_enable profile memory-profiling) \ + $(use_enable static-libs static) \ + $(use_enable static-libs R-static-lib) \ + $(use_with cairo) \ + $(use_with icu ICU) \ + $(use_with jpeg jpeglib) \ + $(use_with lapack) \ + $(use_with !minimal recommended-packages) \ + $(use_with png libpng) \ + $(use_with readline) \ + $(use_with tiff libtiff) \ + $(use_with tk tcltk) \ + $(use_with X x) +} + +src_compile(){ + export VARTEXFONTS="${T}/fonts" + emake + emake -C src/nmath/standalone shared $(use static-libs && echo static) + use doc && emake info pdf +} + +src_install() { + default + emake -C src/nmath/standalone DESTDIR="${D}" install + + if use doc; then + emake DESTDIR="${D}" install-info install-pdf + dosym ../manual /usr/share/doc/${PF}/html/manual + fi + + cat > 99R <<-EOF + LDPATH=${R_DIR}/lib + R_HOME=${R_DIR} + EOF + doenvd 99R + use bash-completion && dobashcomp "${WORKDIR}"/R.bash_completion +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/files/R-2.14.2-library-writability.patch b/dev-lang/R/files/R-2.14.2-library-writability.patch new file mode 100644 index 000000000000..3e6cabf654cc --- /dev/null +++ b/dev-lang/R/files/R-2.14.2-library-writability.patch @@ -0,0 +1,40 @@ +Index: src/library/utils/R/packages2.R +=================================================================== +--- src/library/utils/R/packages2.R (revision 58532) ++++ src/library/utils/R/packages2.R (working copy) +@@ -229,8 +229,8 @@ + domain = NA, immediate. = TRUE) + userdir <- unlist(strsplit(Sys.getenv("R_LIBS_USER"), + .Platform$path.sep))[1L] +- if(interactive() && !file.exists(userdir)) { +- msg <- gettext("Would you like to create a personal library\n%s\nto install packages into?") ++ if(interactive()) { ++ msg <- gettext("Would you like to use a personal library instead?") + if(.Platform$OS.type == "windows") { + ans <- winDialog("yesno", sprintf(msg, sQuote(userdir))) + if(ans != "YES") stop("unable to install packages") +@@ -239,10 +239,21 @@ + if(substr(ans, 1L, 1L) == "n") + stop("unable to install packages") + } +- if(!dir.create(userdir, recursive = TRUE)) +- stop("unable to create ", sQuote(userdir)) + lib <- userdir +- .libPaths(c(userdir, .libPaths())) ++ if(!file.exists(userdir)) { ++ msg <- gettext("Would you like to create a personal library\n%s\nto install packages into?") ++ if(.Platform$OS.type == "windows") { ++ ans <- winDialog("yesno", sprintf(msg, sQuote(userdir))) ++ if(ans != "YES") stop("unable to install packages") ++ } else { ++ ans <- readline(paste(sprintf(msg, userdir), " (y/n) ")) ++ if(substr(ans, 1L, 1L) == "n") ++ stop("unable to install packages") ++ } ++ if(!dir.create(userdir, recursive = TRUE)) ++ stop("unable to create ", sQuote(userdir)) ++ .libPaths(c(userdir, .libPaths())) ++ } + } else stop("unable to install packages") + } + diff --git a/dev-lang/R/files/R-2.14.2-prune-package-update.patch b/dev-lang/R/files/R-2.14.2-prune-package-update.patch new file mode 100644 index 000000000000..8b4b76916e1d --- /dev/null +++ b/dev-lang/R/files/R-2.14.2-prune-package-update.patch @@ -0,0 +1,25 @@ +Index: src/library/utils/R/packages.R +=================================================================== +--- src/library/utils/R/packages.R (revision 58579) ++++ src/library/utils/R/packages.R (working copy) +@@ -323,6 +323,20 @@ + oldPkgs <- old.packages(lib.loc = lib.loc, + contriburl = contriburl, method = method, + available = available, checkBuilt = checkBuilt) ++ ## prune package versions which are invisible to require() ++ if(!is.null(oldPkgs)) { ++ pkg <- 0 ++ while(pkg < nrow(oldPkgs)) { ++ pkg <- pkg + 1 ++ if(find.package(oldPkgs[pkg], lib.loc = lib.loc) != find.package(oldPkgs[pkg], lib.loc = oldPkgs[pkg,2])) { ++ warning(sprintf("package '%s' in library '%s' will not be updated", ++ oldPkgs[pkg], oldPkgs[pkg, 2]), ++ call. = FALSE, immediate. = TRUE) ++ oldPkgs <- oldPkgs[-pkg, , drop = FALSE] ++ pkg <- pkg - 1 ++ } ++ } ++ } + if(is.null(oldPkgs)) + return(invisible()) + } else if (!(is.matrix(oldPkgs) && is.character(oldPkgs))) diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml index 915e03f5b95e..5d205a8da7fb 100644 --- a/dev-lang/R/metadata.xml +++ b/dev-lang/R/metadata.xml @@ -1,8 +1,12 @@ - sci-mathematics - +sci-mathematics + + calchan@gentoo.org + Denis Dupeyron + + R is GNU S, a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run -- cgit v1.2.3-65-gdbad