bioperl: update to 1.7.7
Beware, bioperl has been split in several submodules, please check an exhaustive list of what it implies at: https://metacpan.org/changes/distribution/BioPerl#L71 OK afresh1@
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cwen
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# $OpenBSD: Makefile,v 1.21 2019/07/12 20:43:43 sthen Exp $
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# $OpenBSD: Makefile,v 1.22 2020/08/25 23:56:31 cwen Exp $
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COMMENT= perl tools for bioinformatics
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DISTNAME= BioPerl-1.6.924
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REVISION= 1
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DISTNAME= BioPerl-1.7.7
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PKGNAME= ${DISTNAME:L}# No p5-prefix here.
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CATEGORIES= biology
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HOMEPAGE= https://bioperl.org/
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# perl
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# Perl
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PERMIT_PACKAGE= Yes
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CPAN_AUTHOR= CJFIELDS
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MODULES= cpan
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PKG_ARCH= *
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CPAN_AUTHOR= CJFIELDS
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MODCPAN_EXAMPLES= Yes
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MODCPAN_EXAMPLES_DIR= ${PREFIX}/share/examples/bioperl/
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CONFIGURE_STYLE= modbuild
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RUN_DEPENDS= devel/p5-Data-Stag \
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devel/p5-Error \
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devel/p5-Graph \
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devel/p5-IO-String \
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devel/p5-IO-stringy \
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devel/p5-IPC-Run \
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devel/p5-List-MoreUtils \
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devel/p5-Module-Build \
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devel/p5-Set-Scalar \
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devel/p5-Test-Most \
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devel/p5-Test-RequiresInternet \
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devel/p5-YAML \
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textproc/p5-Libxml \
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textproc/p5-XML-DOM \
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textproc/p5-XML-DOM-XPath \
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textproc/p5-XML-LibXML \
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textproc/p5-XML-SAX \
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textproc/p5-XML-SAX-Base \
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textproc/p5-XML-SAX-Writer \
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textproc/p5-XML-Twig \
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textproc/p5-XML-Writer \
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www/p5-HTTP-Message \
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www/p5-URI \
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www/p5-libwww
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TEST_DEPENDS= devel/p5-Test-Memory-Cycle \
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devel/p5-Test-Weaken
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BUILD_DEPENDS= ${RUN_DEPENDS}
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RUN_DEPENDS= biology/AcePerl \
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databases/p5-DBD-mysql \
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converters/p5-Convert-Binary-C \
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devel/p5-Algorithm-Munkres \
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devel/p5-Array-Compare \
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devel/p5-Class-AutoClass \
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devel/p5-Clone \
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devel/p5-Data-Stag \
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devel/p5-Graph \
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devel/p5-IO-String \
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devel/p5-IO-stringy \
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devel/p5-Set-Scalar \
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devel/p5-Test-Exception \
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devel/p5-Tree-DAG_Node \
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graphics/p5-GD \
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graphics/p5-GD-SVG \
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graphics/p5-SVG-Graph \
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math/p5-GraphViz \
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misc/p5-Spreadsheet-ParseExcel \
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misc/p5-Spreadsheet-WriteExcel \
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textproc/p5-XML-DOM \
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textproc/p5-Libxml \
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textproc/p5-XML-DOM-XPath \
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textproc/p5-XML-Parser \
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textproc/p5-XML-SAX-Writer \
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textproc/p5-XML-Simple \
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textproc/p5-XML-Twig \
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textproc/p5-XML-Writer \
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www/p5-CGI \
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www/p5-HTML-Parser \
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www/p5-SOAP-Lite \
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www/p5-URI \
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www/p5-libwww
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TEST_DEPENDS= devel/p5-Test-Most \
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www/p5-HTML-TableExtract
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MAKE_ENV += TEST_POD=Yes
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MAKE_ENV += TEST_POD=Yes
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# Optional (not ported) dependencies:
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# Postscript-TextBlock
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# Tie-Cacher
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CONFIGURE_ENV+= PERL_MM_USE_DEFAULT=Yes
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PKG_ARCH= *
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.include <bsd.port.mk>
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@ -1,2 +1,2 @@
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SHA256 (BioPerl-1.6.924.tar.gz) = YWp1Rrs8WFBN4nMEoPbLkE4YtrvNtqTshFTyvTe7dtA=
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SIZE (BioPerl-1.6.924.tar.gz) = 12623118
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SHA256 (BioPerl-1.7.7.tar.gz) = cw4r04t1UL9rvVvKUNAZpwzKUUVZcCwTiddw/2nP8bs=
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SIZE (BioPerl-1.7.7.tar.gz) = 7532782
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@ -1,15 +0,0 @@
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$OpenBSD: patch-Bio_Tools_Alignment_Consed_pm,v 1.1 2019/02/21 10:25:48 cwen Exp $
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Fix:
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Error: Can't redeclare "my" in "my"
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Index: Bio/Tools/Alignment/Consed.pm
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--- Bio/Tools/Alignment/Consed.pm.orig
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+++ Bio/Tools/Alignment/Consed.pm
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@@ -1709,7 +1709,7 @@ Recursion is kewl, but this sub should likely be _reve
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sub reverse_recurse($$) {
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- my ($r_source,my $r_destination) = @_;
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+ my ($r_source, $r_destination) = @_;
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if (!@$r_source) {
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return $r_destination;
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}
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@ -1,16 +0,0 @@
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$OpenBSD: patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm,v 1.1 2019/02/21 10:25:48 cwen Exp $
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Avoid some of the super annoying warnings about deprecated braces
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Index: Bio/Tools/SiRNA/Ruleset/tuschl.pm
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--- Bio/Tools/SiRNA/Ruleset/tuschl.pm.orig
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+++ Bio/Tools/SiRNA/Ruleset/tuschl.pm
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@@ -178,8 +178,8 @@ sub _get_oligos {
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my $target = $2;
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# check for too many Gs (or Cs on the other strand)
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- next if ( $target =~ /G{ $self->gstring,}/io );
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- next if ( $target =~ /C{ $self->gstring,}/io );
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+ next if ( $target =~ /G\{ $self->gstring,\}/io );
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+ next if ( $target =~ /C\{ $self->gstring,\}/io );
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# skip Ns (for filtering)
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next if ( $target =~ /N/i);
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@ -1,15 +0,0 @@
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$OpenBSD: patch-maintenance_symlink_script_pl,v 1.2 2019/02/21 10:25:48 cwen Exp $
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Index: maintenance/symlink_script.pl
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--- maintenance/symlink_script.pl.orig
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+++ maintenance/symlink_script.pl
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@@ -12,7 +12,9 @@ my %symlink_scripts = ('bp_bulk_load_gff.pl' => 'bp_pg
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# installation process installs the symlink as the actual file, so we may as
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# well have just done a copy
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-my $install_dir = $build->install_destination('script');
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+my $destdir = $build->runtime_params('destdir');
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+my $install_dir = $destdir . $build->install_destination('script');
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+
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$build->log_info("Will try to install symlinks to $install_dir\n");
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my $orig_dir = $build->cwd;
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chdir($install_dir);
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