commit: 59a04a481c15788a6798996b271efabbbcc78a03 Author: Kent Fredric <kentnl <AT> gentoo <DOT> org> AuthorDate: Tue Jul 9 15:33:53 2019 +0000 Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org> CommitDate: Tue Jul 9 15:35:01 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59a04a48
dev-perl/Boulder: Bulk fixes and fix for bug #678004 - Convert to EAPI6 - Omit Boulder::Store support unless USE=store is specified, as Boulder::Store requires DB_File, which requires perl built with USE="berkdb", and triggering a perl rebuild flipping a use flag could really complicate portage's capacity to solve dependencies, and possibly break your perl. (This is exposed bug bug #678004) - Omit Boulder::Labbase as the module is incomplete, is documented as such, and loads dependencies that aren't available on Gentoo or on CPAN. - Omit Boulder::XML and its dependency on XML-Parser unless USE=xml is specified, as XML handling is not in any way critical to this module. - Remove uncondtional compile-time assertion for XML::Parser - Omit Boulder::Genbank and related assets unless USE=genbank is specified, as this necesarily adds a dependency on dev-perl/CGI as part of its Entrez accessor - Provide examples via USE="examples" Closes: https://bugs.gentoo.org/678004 Package-Manager: Portage-2.3.66, Repoman-2.3.16 Signed-off-by: Kent Fredric <kentnl <AT> gentoo.org> dev-perl/Boulder/Boulder-1.300.0-r2.ebuild | 51 ++++++++++++++++++++++ .../files/Boulder-1.30-no-xml-parser-check.patch | 30 +++++++++++++ dev-perl/Boulder/metadata.xml | 6 ++- 3 files changed, 86 insertions(+), 1 deletion(-) 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 00000000000..a9c75068e9b --- /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/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 00000000000..13ce87969fb --- /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 <[email protected]> +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 31ec77c2000..2971ad7b7ca 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>
