gentoo resync : 11.07.2019

4 files changed, 89 insertions, 2 deletions

diff --git a/dev-perl/Boulder/Boulder-1.300.0-r2.ebuild b/dev-perl/Boulder/Boulder-1.300.0-r2.ebuild
new file mode 100644
index 000000000000..a9c75068e9ba
--- /dev/null
+++ b/dev-perl/Boulder/Boulder-1.300.0-r2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DIST_AUTHOR=LDS
+DIST_VERSION=1.30
+DIST_EXAMPLES=( "eg/*" )
+inherit perl-module
+
+DESCRIPTION="An API for hierarchical tag/value structures"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ia64 ~ppc ~sparc ~x86"
+IUSE="genbank store xml"
+
+RDEPEND="
+	genbank? ( dev-perl/CGI )
+	store? ( virtual/perl-DB_File )
+	xml? ( dev-perl/XML-Parser )
+"
+DEPEND="${RDEPEND}
+	virtual/perl-ExtUtils-MakeMaker
+"
+PATCHES=(
+	"${FILESDIR}/${PN}-${DIST_VERSION}-no-xml-parser-check.patch"
+)
+PERL_RM_FILES=(
+	# Incomplete, instructs not to use, deps not in Gentoo
+	"Boulder/Labbase.pm"
+)
+src_prepare() {
+	use xml || PERL_RM_FILES+=(
+		"Boulder/XML.pm"
+	)
+	use genbank || PERL_RM_FILES+=(
+		"Boulder/Genbank.pm"
+		"Stone/GB_Sequence.pm"
+		"doc/genbank_tags.txt"
+		"eg/gb_get"
+		"eg/gb_search"
+		"eg/genbank.pl"
+		"eg/genbank2.pl"
+		"eg/genbank3.pl"
+	)
+	use store || PERL_RM_FILES+=(
+		"Boulder/Store.pm"
+		"t/store.t"
+	)
+	perl-module_src_prepare
+}
diff --git a/dev-perl/Boulder/Manifest b/dev-perl/Boulder/Manifest
index 2690d5aba887..99813608eb65 100644
--- a/dev-perl/Boulder/Manifest
+++ b/dev-perl/Boulder/Manifest
@@ -1,3 +1,5 @@
+AUX Boulder-1.30-no-xml-parser-check.patch 795 BLAKE2B e109ec3a4ec7bd29e06c41e8aad25d70a58a5f63546bfd18f1d81ad99a208495a1a94c0bf8a86743f234104b4915749ce3aa0ad0c2e85939d05e8c8084e90a56 SHA512 d4baa7f9b1d2b3e0ace66cb3e3508ed9f711dd9786a0af1fb030b1d2cd8acda1337bea8004a1e1799fb3706bc7c742a1691a0ae5c97d00af774ed9939cc62459
 DIST Boulder-1.30.tar.gz 91202 BLAKE2B e1c7f44248d9b257669713b0168b395cad73713476c0cbf688c1513f99552cafc428c7118bdc13ec33018d198434d36d76cbbfe06308d17df230c951ce85c8d2 SHA512 787c80fb578afd8495e57d96f4db69c6d02f69957593cae9e1e130f58f6b34b79bebe60e2484e6cbc81906e60f79df0f55e9479cffc5c0b800c00c6946d5479e
 EBUILD Boulder-1.300.0-r1.ebuild 355 BLAKE2B a8d50b85f2eb88709541016901cbb11406b5388715ff48216d9c83a584ea94dae88b3e008f5171c1575a2d5a162a81f20e1ce3b8b0e41a2e7e6441297307de0f SHA512 f2165a70f9a29578453e7c6888306ae95e4b67e574b26c401924884240e3597786781912758cc32ca6b1ad620320a7a6e10a348b140cbc334cd15daa7f3f2d14
-MISC metadata.xml 1992 BLAKE2B 996bfe3a5f2f3a5b95af031d34eb36ae507ae76324f45ee32e5868b435000cbe253dc8df0fd67320718e6f5a8b9fb1913d6b49148b83f2a6aef69ec538ede544 SHA512 9530e1dac2e2c3aa10c9f5b0021e273af9ebb0b2c4a306645c3490235eb3e729819c84454c7d4272c82aaec7657640978cde84ca3750ed498d160b23c5f704c2
+EBUILD Boulder-1.300.0-r2.ebuild 1015 BLAKE2B 8a54e30b606df33b1481e65145d7668a4ee48859691e6de7f9e411277d370701323b5999bc15a96c4bf21448f18e7b3ea628fcd689d87439c21f83d93c5bc041 SHA512 605e04e6ae1eeb08ffc370decb879335c97d366d9b531e12f3768802b67af269a7be2b4ad418c862e3b7e569149d0955278f67da34452ead1d9ce474be889f44
+MISC metadata.xml 2146 BLAKE2B 9c6b153e95557ea6731498a942462f4276b69978209d15a840ddd1d28381a7ea461a154cffd519fbc10f796d1cab3429832aa17b4e9e4208fc555145e1bbea9a SHA512 67e0a72cc4203933d8ec3cc01a7585bd78b0fe2b1045670e4d271f43c4f4ed3ae001611d27f8aa09b9ac30e5a664fe8b3f2699978d0e6f9dd859bde4e0a0d1d1
diff --git a/dev-perl/Boulder/files/Boulder-1.30-no-xml-parser-check.patch b/dev-perl/Boulder/files/Boulder-1.30-no-xml-parser-check.patch
new file mode 100644
index 000000000000..13ce87969fb1
--- /dev/null
+++ b/dev-perl/Boulder/files/Boulder-1.30-no-xml-parser-check.patch
@@ -0,0 +1,30 @@
+From 82eaa751a4aebb6cce70b83407c1fafd13334130 Mon Sep 17 00:00:00 2001
+From: Kent Fredric <kentnl@gentoo.org>
+Date: Wed, 10 Jul 2019 02:58:13 +1200
+Subject: Remove hardcoded XML::Parser check
+
+This test isn't necessary and is a vestigal side effect of old build
+chains that didn't have prereqs.
+
+As this dependency is only needed if you're using Boulder::XML, its
+rather redundant.
+---
+ Makefile.PL | 3 ---
+ 1 file changed, 3 deletions(-)
+
+diff --git a/Makefile.PL b/Makefile.PL
+index 2fe3176..245f16e 100644
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -1,8 +1,5 @@
+ use ExtUtils::MakeMaker;
+ 
+-eval "use XML::Parser; 1" 
+-  || warn "XML::Parser module not found.  This module is required to use Boulder::XML\n";
+-
+ WriteMakefile(
+     'NAME'	=> 'Boulder',
+     'DISTNAME'  => 'Boulder',
+-- 
+2.22.0
+
diff --git a/dev-perl/Boulder/metadata.xml b/dev-perl/Boulder/metadata.xml
index 31ec77c20009..2971ad7b7ca4 100644
--- a/dev-perl/Boulder/metadata.xml
+++ b/dev-perl/Boulder/metadata.xml
@@ -12,7 +12,6 @@
     <remote-id type="cpan-module">Boulder::Blast::NCBI</remote-id>
     <remote-id type="cpan-module">Boulder::Blast::WU</remote-id>
     <remote-id type="cpan-module">Boulder::Genbank</remote-id>
-    <remote-id type="cpan-module">Boulder::Labbase</remote-id>
     <remote-id type="cpan-module">Boulder::LocusLink</remote-id>
     <remote-id type="cpan-module">Boulder::Medline</remote-id>
     <remote-id type="cpan-module">Boulder::Omim</remote-id>
@@ -35,4 +34,9 @@
     <remote-id type="cpan-module">UnigeneAccessor</remote-id>
     <remote-id type="cpan-module">Yank</remote-id>
   </upstream>
+  <use>
+    <flag name="genbank">Provide support with Boulder::Genbank for decoding Genbank data records</flag>
+    <flag name="store">Provide support with Boulder::Store for persisting Stone objects</flag>
+  </use>
+
 </pkgmetadata>