dev-lang/R: add 4.2.2

My upstream patches to the R_BROWSER and R_PDFVIEWER search order didn't
land in this release, but we're already running eautoreconf, so we might
as well include them. This lets us drop the dependency on xdg-utils, and
remove the stanza (conditional on USE=X) that sets the default browser
and viewer to xdg-open.

We are also able to drop a patch to the test suite that was merged
upstream.

Closes: https://bugs.gentoo.org/458176
Closes: https://bugs.gentoo.org/879863
Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

3 files changed, 342 insertions, 0 deletions

diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 8895d614d77a..b3d53118aec4 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -1,2 +1,3 @@
 DIST R-4.2.1.tar.gz 37601544 BLAKE2B b898262a05c92e125c36a661a89be34b1698177832002f7aa21ccfcf0b30a06481e2154eea9e77a94b1ad8ca35c7bc4aead2be99b862dca7450acee1bec6a99f SHA512 c1baf46d22304c425dde79301183f80f99f2752300137b0b6f902c3e55e2419d5e9185c97de6e3c840a38f6345a6c334aa24161656d4a7f6fa01570390f1122f
+DIST R-4.2.2.tar.gz 33987014 BLAKE2B 083d07b055308451e32133d378abc4aea7dd6da341554dca96ed5863fe2bc937aa3faa94bbd8d3620d3e6e020f806975cbc375ca28c599bd645267b97b2a49d4 SHA512 abbf1c7d016f8e1a9a0c4ad5dee2509a164449da34729f3e98d99ad8678ab398005fb8ed20288d4a6ed1e46ad4c70ad246f31a1a07aab99ba8fc6a5f02e1a309
 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
diff --git a/dev-lang/R/R-4.2.2.ebuild b/dev-lang/R/R-4.2.2.ebuild
new file mode 100644
index 000000000000..f7daf9d87167
--- /dev/null
+++ b/dev-lang/R/R-4.2.2.ebuild
@@ -0,0 +1,246 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 autotools flag-o-matic fortran-2 toolchain-funcs
+
+# latest git commit for R bash completion:
+#   https://github.com/deepayan/rcompletion
+BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6
+
+DESCRIPTION="Language and environment for statistical computing and graphics"
+HOMEPAGE="https://www.r-project.org/"
+SRC_URI="
+	mirror://cran/src/base/R-4/${P}.tar.gz
+	https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64 ~hppa ~ia64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="cairo doc icu java jpeg lapack lto minimal nls openmp perl png prefix profile readline test tiff tk X"
+
+REQUIRED_USE="
+	png? ( || ( cairo X ) )
+	jpeg? ( || ( cairo X ) )
+	tiff? ( || ( cairo X ) )"
+RESTRICT="
+	minimal? ( test )
+	!test? ( test )"
+
+# At least one package installation in the test suite requires TeX,
+# and will fail without it (bug #718056).
+DEPEND="
+	app-arch/bzip2
+	app-arch/xz-utils
+	app-text/ghostscript-gpl
+	dev-libs/libpcre2:=
+	>=dev-libs/tre-0.8.0_p20210321[approx]
+	net-misc/curl
+	virtual/blas
+	sys-libs/zlib[minizip]
+	|| (
+		sys-apps/coreutils
+		app-misc/realpath
+	)
+	cairo? (
+		x11-libs/cairo:=[X=]
+		x11-libs/pango:=
+	)
+	icu? ( dev-libs/icu:= )
+	jpeg? ( media-libs/libjpeg-turbo:= )
+	kernel_linux? ( net-libs/libtirpc )
+	lapack? ( virtual/lapack )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng:= )
+	readline? ( sys-libs/readline:= )
+	tiff? ( media-libs/tiff:= )
+	tk? ( dev-lang/tk:= )
+	X? (
+		x11-libs/libXmu
+		x11-libs/libXt
+	)"
+RDEPEND="${DEPEND}
+	java? ( >=virtual/jre-1.8:* )"
+BDEPEND="
+	virtual/pkgconfig
+	doc? (
+		virtual/latex-base
+		dev-texlive/texlive-fontsrecommended
+	)
+	test? ( virtual/latex-base )"
+
+PATCHES=(
+	"${FILESDIR}"/R-3.4.1-parallel.patch
+	"${FILESDIR}"/R-3.4.1-rmath-shared.patch
+	"${FILESDIR}"/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch
+	"${FILESDIR}"/R-3.6.2-no-gzip-doc.patch
+	"${FILESDIR}"/R-4.2.2-browser-pdf-prefs.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	if [[ ${MERGE_TYPE} != binary ]] && use openmp; then
+		tc-check-openmp
+		FORTRAN_NEED_OPENMP=1
+	fi
+
+	fortran-2_pkg_setup
+
+	# avoid using existing R installation
+	unset R_HOME
+}
+
+src_prepare() {
+	default
+
+	# fix packages.html for doc (gentoo bug #205103)
+	sed -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \
+		-i src/library/tools/R/Rd.R || die
+
+	# fix Rscript path when installed (gentoo bug #221061)
+	sed -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${EPREFIX}/usr/$(get_libdir)/${PN}\"':" \
+		-i src/unix/Makefile.in || die "sed unix Makefile failed"
+
+	# fix HTML links to manual (gentoo bug #273957)
+	sed -e 's:\.\./manual/:manual/:g' \
+		-i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
+
+	use lapack &&
+		export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	use perl &&
+		export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}"
+
+	# don't search /usr/local
+	sed -i -e '/FLAGS=.*\/local\//c\: # removed by ebuild' configure.ac || die
+
+	# Fix for Darwin (macOS)
+	if use prefix; then
+		if [[ ${CHOST} == *-darwin* ]] ; then
+			sed -e 's:-install_name libR.dylib:-install_name ${libdir}/R/lib/libR.dylib:' \
+				-e 's:-install_name libRlapack.dylib:-install_name ${libdir}/R/lib/libRlapack.dylib:' \
+				-e 's:-install_name libRblas.dylib:-install_name ${libdir}/R/lib/libRblas.dylib:' \
+				-e "/SHLIB_EXT/s/\.so/.dylib/" \
+				-i configure.ac || die
+			# sort of "undo" 2.14.1-rmath-shared.patch
+			sed -e "s:-Wl,-soname=libRmath.so:-install_name ${EPREFIX}/usr/$(get_libdir)/libRmath.dylib:" \
+				-i src/nmath/standalone/Makefile.in || die
+		else
+			append-ldflags -Wl,-rpath="${EPREFIX}/usr/$(get_libdir)/R/lib"
+		fi
+	fi
+
+	AT_M4DIR=m4 eautoreconf
+}
+
+src_configure() {
+	filter-ldflags -Wl,-Bdirect -Bdirect
+
+	econf \
+		--enable-byte-compiled-packages \
+		--enable-R-shlib \
+		--disable-R-framework \
+		--disable-R-static-lib \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
+		--with-system-tre \
+		$(use_enable java) \
+		$(use_enable lto lto R) \
+		$(use_enable nls) \
+		$(use_enable openmp) \
+		$(use_enable profile R-profiling) \
+		$(use_enable profile memory-profiling) \
+		$(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) \
+		$(use_with tk tk-config "${ESYSROOT}"/usr/$(get_libdir)/tkConfig.sh) \
+		$(use_with tk tcl-config "${ESYSROOT}"/usr/$(get_libdir)/tclConfig.sh) \
+		$(use_with X x)
+}
+
+src_compile() {
+	export VARTEXFONTS="${T}"/fonts
+	emake AR="$(tc-getAR)"
+	emake -C src/nmath/standalone shared AR="$(tc-getAR)"
+	use doc && emake info pdf
+}
+
+src_install() {
+	default
+	emake -j1 -C src/nmath/standalone DESTDIR="${D}" install
+
+	if use doc; then
+		emake DESTDIR="${D}" install-info install-pdf
+		dosym ../manual /usr/share/doc/${PF}/html/manual
+	fi
+
+	newenvd - 99R <<-_EOF_
+		LDPATH="${EPREFIX}/usr/$(get_libdir)/${PN}/lib"
+		R_HOME="${EPREFIX}/usr/$(get_libdir)/${PN}"
+	_EOF_
+
+	newbashcomp "${DISTDIR}"/${PN}-${BCPV}.bash_completion ${PN}
+	# The buildsystem has a different understanding of install_names than
+	# we require.  Since it builds modules like shared objects (wrong), many
+	# objects (all modules) get an incorrect install_name.  Fixing the build
+	# system here is not really trivial.
+	if [[ ${CHOST} == *-darwin* ]] ; then
+		local mod
+		pushd "${ED}"/usr/$(get_libdir)/R >/dev/null || die
+		for mod in $(find . -name "*.dylib") ; do
+			mod=${mod#./}
+			install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" "${mod}"
+		done
+		popd >/dev/null || die
+	fi
+
+	# Users are encouraged to access some of the the R documentation
+	# interactively, through functions like "contributors()" that
+	# tries to open the "AUTHORS" file. Other files can be accessed
+	# by name with RShowDoc(), and the documentation for e.g. license()
+	# and RShowDoc() suggests a few of these names. Here we try to
+	# collect as many names as possible that a user might actually
+	# try to view through R, because if we don't decompress them,
+	# then R doesn't know what to do with 'em. Bug #556706.
+	local INTERACTIVE_DOCS=(
+		AUTHORS
+		COPYING
+		FAQ
+		NEWS
+		THANKS
+	)
+
+	# Other data sources that are shipped as "documentation," but which
+	# need to be accessible via their original unmolested filenames.
+	local INTERACTIVE_DATA=(
+		BioC_mirrors.csv
+		CRAN_mirrors.csv
+		KEYWORDS.db
+		NEWS.rds
+	)
+
+	local f NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" )
+	for f in "${NOCOMPRESS_DOCS[@]}"; do
+		docompress -x /usr/share/doc/${PF}/${f}
+	done
+
+	# Finally, an extra copy of this started showing up at some point...
+	rm "${ED}"/usr/$(get_libdir)/R/COPYING || die
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}
diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
new file mode 100644
index 000000000000..b5a953cb6057
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
@@ -0,0 +1,95 @@
+From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:31:46 -0400
+Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER.
+
+The xdg-open utility (if it is present) will launch the user's
+preferred browsr or PDF viewer when fed an HTML page or a PDF
+document, respectively. It therefore makes sense to prefer it over
+(for example) firefox, which may be installed but not the user's
+preferred browser.
+---
+ m4/R.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index bdcfbea..c5052e7 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -237,7 +237,7 @@ fi])
+ ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open
+ AC_DEFUN([R_PROG_BROWSER],
+ [if test -z "${R_BROWSER}"; then
+-  AC_PATH_PROGS(R_BROWSER, [firefox mozilla galeon opera xdg-open kfmclient gnome-moz-remote open])
++  AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla galeon opera kfmclient gnome-moz-remote open])
+ fi
+ if test -z "${R_BROWSER}"; then
+   warn_browser="I could not determine a browser"
+@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER)
+ ## the FreeBSD acroread port.
+ AC_DEFUN([R_PROG_PDFVIEWER],
+ [AC_PATH_PROGS(R_PDFVIEWER,
+-               [${R_PDFVIEWER} acroread acroread4 xdg-open evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview])
++               [${R_PDFVIEWER} xdg-open acroread acroread4 evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview])
+ if test -z "${R_PDFVIEWER}"; then
+   warn_pdfviewer="I could not determine a PDF viewer"
+   AC_MSG_WARN([${warn_pdfviewer}])
+-- 
+2.35.1
+
+From 4e50ed9c976a4422a6d431d3d078164948f26bda Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:36:41 -0400
+Subject: [PATCH 2/3] m4/R.m4: add epiphany, lynx, and links to the R_BROWSER
+ search list.
+
+The epiphany browser is today one of the more popular ones, being the
+"official" GNOME browser. And lynx and links are nice text-based
+fallbacks.
+---
+ m4/R.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index c5052e7..e99b0f9 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -237,7 +237,7 @@ fi])
+ ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open
+ AC_DEFUN([R_PROG_BROWSER],
+ [if test -z "${R_BROWSER}"; then
+-  AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla galeon opera kfmclient gnome-moz-remote open])
++  AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla epiphany galeon opera kfmclient gnome-moz-remote open lynx links])
+ fi
+ if test -z "${R_BROWSER}"; then
+   warn_browser="I could not determine a browser"
+-- 
+2.35.1
+
+From 719294ed2548f79ab6a5861662716d853284f4d7 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:38:03 -0400
+Subject: [PATCH 3/3] m4/R.m4: add atril to the R_PDFVIEWER list.
+
+Atril is the PDF viewer for the MATE desktop, essentially a fork of
+the gnome-2.x evince viewer.
+---
+ m4/R.m4 | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index e99b0f9..7e04ced 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER)
+ ## the FreeBSD acroread port.
+ AC_DEFUN([R_PROG_PDFVIEWER],
+ [AC_PATH_PROGS(R_PDFVIEWER,
+-               [${R_PDFVIEWER} xdg-open acroread acroread4 evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview])
++               [${R_PDFVIEWER} xdg-open acroread acroread4 evince atril xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview])
+ if test -z "${R_PDFVIEWER}"; then
+   warn_pdfviewer="I could not determine a PDF viewer"
+   AC_MSG_WARN([${warn_pdfviewer}])
+-- 
+2.35.1
+