Version bump. Add patches to fix handling of library writability and package updates.

Package-Manager: portage-2.1.10.49/cvs/Linux x86_64

6 files changed, 245 insertions, 15 deletions

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 <calchan@gentoo.org> +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 <bicatali@gentoo.org> 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
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+EBUILD R-2.14.2.ebuild 4413 RMD160 fc99894f788fb824bd36e2650e29359a2f67acf4 SHA1 3637ba3e35918917192b2c6534d3c60b83be7d01 SHA256 a30c20572426d6df161ebfe2ad47ee53298dfed6bf4d9a5cd0ea434cf7f33932
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+MISC metadata.xml 1124 RMD160 b1816af77325d46cb8670e0d23ea8b367b0b67f2 SHA1 631740a32ccdd45b3991d855b9cc44cd5e570507 SHA256 8f06d05ef29fdd4960269413a7e3e6ed5cfbdf32fa7cac5ed4c2750d58a4785b
diff --git a/dev-lang/R/R-2.14.2.ebuild b/dev-lang/R/R-2.14.2.ebuild
new file mode 100644
index 000000000000..235605c092b7
--- /dev/null
+++ b/dev-lang/R/R-2.14.2.ebuild
@@ -0,0 +1,159 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.14.2.ebuild,v 1.1 2012/03/05 17:23:05 calchan Exp $
+
+EAPI=4
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 versionator
+
+DESCRIPTION="Language and environment for statistical computing and graphics"
+HOMEPAGE="http://www.r-project.org/"
+SRC_URI="mirror://cran/src/base/R-2/${P}.tar.gz
+	bash-completion? ( mirror://gentoo/R.bash_completion.bz2 )"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd"
+IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="app-arch/bzip2
+	app-text/ghostscript-gpl
+	dev-libs/libpcre
+	virtual/blas
+	virtual/fortran
+	cairo? ( x11-libs/cairo[X] x11-libs/pango )
+	icu? ( dev-libs/icu )
+	jpeg? ( virtual/jpeg )
+	lapack? ( virtual/lapack )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng )
+	readline? ( sys-libs/readline )
+	tk? ( dev-lang/tk )
+	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
+
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig
+	doc? (
+			virtual/latex-base
+			dev-texlive/texlive-fontsrecommended
+		 )"
+
+RDEPEND="${CDEPEND}
+	( || ( <sys-libs/zlib-1.2.5.1-r1 >=sys-libs/zlib-1.2.5.1-r2[minizip] ) )
+	app-arch/xz-utils
+	java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+R_DIR="${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 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-mathematics</herd>
-	<longdescription lang="en">
+<herd>sci-mathematics</herd>
+<maintainer>
+  <email>calchan@gentoo.org</email>
+  <name>Denis Dupeyron</name>
+</maintainer>
+<longdescription lang="en">
   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