gentoo resync : 14.07.2018

6 files changed, 264 insertions, 0 deletions

diff --git a/dev-perl/Ace/Ace-1.920.0-r3.ebuild b/dev-perl/Ace/Ace-1.920.0-r3.ebuild
new file mode 100644
index 000000000000..9b035a9c5ae0
--- /dev/null
+++ b/dev-perl/Ace/Ace-1.920.0-r3.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DIST_NAME=AcePerl
+DIST_AUTHOR=LDS
+DIST_VERSION=1.92
+DIST_EXAMPLES=("examples/*")
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="Object-Oriented Access to ACEDB Databases"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="test"
+
+RDEPEND="virtual/perl-Digest-MD5
+	dev-perl/Cache-Cache
+	dev-perl/GD
+	elibc_glibc? ( net-libs/libtirpc net-libs/rpcsvc-proto )
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	eapply "${FILESDIR}/${PN}-1.92-rpcxs.patch"
+	eapply "${FILESDIR}/${PN}-1.92-gcc-nonvoid.patch"
+
+	cat > "${S}/acelib/wmake/DARWIN_DEF" <<EOF
+NAME = DARWIN
+COMPILER = $(tc-getCC) -fwritable-strings -DACEDB4 -DPOSIX
+LINKER = $(tc-getLD)
+
+LIBS = -lm
+
+EOF
+
+	if use elibc_glibc ; then
+		eapply "${FILESDIR}/${PN}-1.92-glibc26.patch"
+		export LIBS="-ltirpc"
+	fi
+
+	export MAKEOPTS="-j1"
+	perl-module_src_prepare
+}
+
+src_test() {
+	local MODULES=(
+		"Ace ${DIST_VERSION}"
+		"Ace::Freesubs 1.00"
+		"Ace::Graphics::Fk" # NO VERSION
+		"Ace::Graphics::Glyph"
+		"Ace::Graphics::Glyph::anchored_arrow"
+		"Ace::Graphics::Glyph::arrow"
+		"Ace::Graphics::Glyph::box"
+		"Ace::Graphics::Glyph::crossbox"
+		"Ace::Graphics::Glyph::dot"
+		"Ace::Graphics::Glyph::ex"
+		"Ace::Graphics::Glyph::graded_segments"
+		"Ace::Graphics::Glyph::group"
+		"Ace::Graphics::Glyph::line"
+		"Ace::Graphics::Glyph::primers"
+		"Ace::Graphics::Glyph::segments"
+		"Ace::Graphics::Glyph::span"
+		"Ace::Graphics::Glyph::toomany"
+		"Ace::Graphics::Glyph::transcript"
+		"Ace::Graphics::Glyph::triangle"
+		"Ace::Graphics::GlyphFactory"
+		"Ace::Graphics::Panel"
+		"Ace::Graphics::Track"
+		"Ace::Iterator 1.51"
+		"Ace::Local 1.05"
+		"Ace::Model 1.51"
+		"Ace::Object 1.66"
+		"Ace::Object::Wormbase"
+		"Ace::RPC 1.00"
+		"Ace::Sequence 1.51"
+		"Ace::Sequence::Feature"
+		"Ace::Sequence::FeatureList"
+		"Ace::Sequence::GappedAlignment 1.20"
+		"Ace::Sequence::Gene"
+		"Ace::Sequence::Homol"
+		"Ace::Sequence::Multi"
+		"Ace::Sequence::Transcript"
+		"Ace::SocketServer 1.01"
+		"GFF::Filehandle"
+# Need Ace::Browser
+# 		"Ace::Browser::AceSubs ${DIST_VERSION}"
+#		"Ace::Browser::GeneSubs ${DIST_VERSION}"
+#		"Ace::Browser::SearchSubs ${DIST_VERSION}"
+#		"Ace::Browser::SiteDefs ${DIST_VERSION}"
+#		"Ace::Browser::TreeSubs ${DIST_VERSION}"
+	)
+	local failed=()
+	for dep in "${MODULES[@]}"; do
+		ebegin "Compile testing ${dep}"
+			perl -Mblib="${S}" -M"${dep} ()" -e1
+		eend $? || failed+=( "$dep" )
+	done
+	if [[ ${failed[@]} ]]; then
+		echo
+		eerror "One or more modules failed compile:";
+		for dep in "${failed[@]}"; do
+			eerror "  ${dep}"
+		done
+		die "Failing due to module compilation errors";
+	fi
+	if ! has "network" "${DIST_TEST_OVERRIDE:-${DIST_TEST:-do parallel}}"; then
+		ewarn "This package needs network access to run its full test suite"
+		ewarn "For details, see:"
+		ewarn "https://wiki.gentoo.org/wiki/Project:Perl/maint-nodes/dev-perl/Ace"
+	else
+		perl-module_src_test
+	fi
+}
diff --git a/dev-perl/Ace/Manifest b/dev-perl/Ace/Manifest
new file mode 100644
index 000000000000..681bb24e002a
--- /dev/null
+++ b/dev-perl/Ace/Manifest
@@ -0,0 +1,6 @@
+AUX Ace-1.92-gcc-nonvoid.patch 729 BLAKE2B d98d4d2925f8f10f55f64c945ff61509c3ba9fe585432623b97d50eb65ae827ad30e03b653d0e3c2cc7de7bdedff5e312b5383ca303a24c6aa2f5cd95f0bbb81 SHA512 69b2c93de2457aee9908374c475ae2c3aa3e03bcec807abe86ba0a39d28ee41ea2d0a6aaebe99067e50f044933e6b19ea16d1c6e0bd6423b4bb54bf09bf30e90
+AUX Ace-1.92-glibc26.patch 749 BLAKE2B 261d699ab79bb625cf8590c900913ee35363b7cd7a70d3ec82a3866c9e06c33e70f760610b65e2591b1becbff5b58264c61917628cddbd8a2d490ea6c4911e0d SHA512 a383275a27abaf533174395040513dc47355a1c56d660d7221e4142ea90a1ca97957f8fd981476ec62744df7a65037b44ad957467962ce5aa730f2fba916f7d1
+AUX Ace-1.92-rpcxs.patch 819 BLAKE2B 2eb978b7bbced6b67976685d8102724f6357983459e90a14fdab1cb696a8e8c033093d3427cf7aec820aa27eb0f71c9d505962dc2aa62ca67455562b869a5179 SHA512 ae26f67a5a0b91652c90dbb4beea7553e3affc40a15db52247ba28e4171f150c4ffa70ce15b69ce3735176c810b36105b00fb5675f4320340354a929568b49d9
+DIST AcePerl-1.92.tar.gz 300163 BLAKE2B 4fac4d7f56d31f179a1a310688cde078371a1e6605b229016a5a2f3a32de01bf3421c459eeefcdfdd12df3baf34d6495c8e7998e1c66a47215ea2abd741303b6 SHA512 0db8392336dd48c58bdaf8d8d9ac6d1106124259f27fa95951aa8d496014e1e8b89ed87f6df276473e3bcb44a8d323f864178a9b84dd1e787d614bd0b8e93be9
+EBUILD Ace-1.920.0-r3.ebuild 2926 BLAKE2B c6ee969eaea5761d58588914b259bffa66f25380c5cc6448020ccd8d07328f7a604e7ec3050c6879007edafe14c7fbe412a8bd24de60b8ea9e6c85a5c7754ae2 SHA512 3c6dd7ec9f2c1caf39a8d0aa408b4ecb684d13874246399a22138c07645613ccb519eb2166674bcad59d0b80e2c4b886cfb0e3fbc28ff25edc2895fd37fcae4b
+MISC metadata.xml 3416 BLAKE2B 4385d220ac60f2e41750bb1afeff4f9a9055526710db08c2688f1e3787a17f2d9943af22825c8ec554c832f2a428410578baf25044348cbc984114890adcc770 SHA512 aa3443c187165f3cf97e7110238cb039242345071f9e3f74ed40e39a9ce0720062706dd78539eff1553703ed5e8cf55d42b924ebae3cc992366358d300ec544d
diff --git a/dev-perl/Ace/files/Ace-1.92-gcc-nonvoid.patch b/dev-perl/Ace/files/Ace-1.92-gcc-nonvoid.patch
new file mode 100644
index 000000000000..78c0572ed6ff
--- /dev/null
+++ b/dev-perl/Ace/files/Ace-1.92-gcc-nonvoid.patch
@@ -0,0 +1,31 @@
+From c36659030eab65bcf7017e099377bf87a04d1667 Mon Sep 17 00:00:00 2001
+From: Anton Molyboha <anton.stay.connected@gmail.com>
+Date: Fri, 10 Nov 2017 17:37:54 -0500
+Subject: Fix compile with newer gcc "non-void function 'constant' should ..."
+
+Bug: https://bugs.gentoo.org/637330
+Bug: https://rt.cpan.org/Ticket/Display.html?id=123593
+---
+ RPC/RPC.xs | 6 ------
+ 1 file changed, 6 deletions(-)
+
+diff --git a/RPC/RPC.xs b/RPC/RPC.xs
+index 3e059c0..cd4f6fa 100644
+--- a/RPC/RPC.xs
++++ b/RPC/RPC.xs
+@@ -152,12 +152,6 @@ int arg;
+     case 'Z':
+ 	break;
+     case '_':
+-	if (strEQ(name, "_ACECLIENT_"))
+-#ifdef _ACECLIENT_
+-	    return _ACECLIENT_;
+-#else
+-	    goto not_there;
+-#endif
+ 	break;
+     }
+     errno = EINVAL;
+-- 
+2.16.2
+
diff --git a/dev-perl/Ace/files/Ace-1.92-glibc26.patch b/dev-perl/Ace/files/Ace-1.92-glibc26.patch
new file mode 100644
index 000000000000..93913485b2f4
--- /dev/null
+++ b/dev-perl/Ace/files/Ace-1.92-glibc26.patch
@@ -0,0 +1,29 @@
+From 79cbe4803f73eab5474e709b20ed570a44071182 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Andreas=20K=2E=20H=C3=BCttel?= <dilfridge@gentoo.org>
+Date: Sat, 31 Mar 2018 08:12:32 +1300
+Subject: Fix building with GlibC 2.26
+
+Bug: https://bugs.gentoo.org/637114
+---
+ acelib/wmake/LINUX_DEF | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/acelib/wmake/LINUX_DEF b/acelib/wmake/LINUX_DEF
+index ba96774..bd89334 100644
+--- a/acelib/wmake/LINUX_DEF
++++ b/acelib/wmake/LINUX_DEF
+@@ -18,9 +18,9 @@
+ NAME = LINUX
+ COMPILER = gcc -g -Wall -O2 -DACEDB4
+ LINKER = gcc -g
+-USEROPTS=-fPIC
++USEROPTS=-I/usr/include/tirpc -fPIC
+ 
+-LIBS = -lm
++LIBS = -ltirpc -lm
+ Xt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11
+ LEX_LIBS = 
+ 
+-- 
+2.16.2
+
diff --git a/dev-perl/Ace/files/Ace-1.92-rpcxs.patch b/dev-perl/Ace/files/Ace-1.92-rpcxs.patch
new file mode 100644
index 000000000000..be67f6fe1168
--- /dev/null
+++ b/dev-perl/Ace/files/Ace-1.92-rpcxs.patch
@@ -0,0 +1,25 @@
+From f44e3b39758057e3a5af7654768d40de2b249ae5 Mon Sep 17 00:00:00 2001
+From: Kent Fredric <kentnl@gentoo.org>
+Date: Fri, 13 Oct 2017 17:30:57 +1300
+Subject: Enable RPC and XS support
+
+---
+ Makefile.PL | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Makefile.PL b/Makefile.PL
+index 232bc42..7a312fd 100644
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -10,7 +10,7 @@ while (!$choice) {
+ 		  "  1) Interface to Ace socket server and local databases (pure Perl)\n" .
+ 		  "  2) The above plus XS optimizations (requires C compiler)\n" .
+ 		  "  3) The above plus RPC server interface (requires C compiler)\n\n" .
+-		  "Enter your choice: ", "1");
++		  "Enter your choice: ", "3");
+   if ($reply =~ /(\d+)/) {
+     $choice = $1;
+     die "invalid choice: $choice!" if $choice < 1  ||  $choice > 3;
+-- 
+2.16.2
+
diff --git a/dev-perl/Ace/metadata.xml b/dev-perl/Ace/metadata.xml
new file mode 100644
index 000000000000..5d700f3b63b0
--- /dev/null
+++ b/dev-perl/Ace/metadata.xml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>perl@gentoo.org</email>
+    <name>Gentoo Perl Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="cpan">AcePerl</remote-id>
+    <remote-id type="cpan-module">Ace</remote-id>
+    <remote-id type="cpan-module">Ace::Browser::AceSubs</remote-id>
+    <remote-id type="cpan-module">Ace::Browser::GeneSubs</remote-id>
+    <remote-id type="cpan-module">Ace::Browser::SearchSubs</remote-id>
+    <remote-id type="cpan-module">Ace::Browser::SiteDefs</remote-id>
+    <remote-id type="cpan-module">Ace::Browser::TreeSubs</remote-id>
+    <remote-id type="cpan-module">Ace::Freesubs</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Fk</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::anchored_arrow</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::arrow</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::box</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::crossbox</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::dot</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::ex</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::graded_segments</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::group</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::line</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::primers</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::segments</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::span</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::toomany</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::transcript</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Glyph::triangle</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::GlyphFactory</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Panel</remote-id>
+    <remote-id type="cpan-module">Ace::Graphics::Track</remote-id>
+    <remote-id type="cpan-module">Ace::Iterator</remote-id>
+    <remote-id type="cpan-module">Ace::Local</remote-id>
+    <remote-id type="cpan-module">Ace::Model</remote-id>
+    <remote-id type="cpan-module">Ace::Object</remote-id>
+    <remote-id type="cpan-module">Ace::Object::Wormbase</remote-id>
+    <remote-id type="cpan-module">Ace::RPC</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::Feature</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::FeatureList</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::GappedAlignment</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::Gene</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::Homol</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::Multi</remote-id>
+    <remote-id type="cpan-module">Ace::Sequence::Transcript</remote-id>
+    <remote-id type="cpan-module">Ace::SocketServer</remote-id>
+    <remote-id type="cpan-module">GFF::Filehandle</remote-id>
+  </upstream>
+</pkgmetadata>