Index: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm =================================================================== --- head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm (revision 493446) +++ head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm (nonexistent) @@ -1,80 +0,0 @@ ---- Bio/Root/Build.pm.orig 2014-07-10 20:13:23 UTC -+++ Bio/Root/Build.pm -@@ -83,49 +83,9 @@ - } - } - closedir($scripts_dir); -- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ". -- "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ". -- "or [n]one?"; -- -- my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); -- -- if ($prompt =~ /^[aA]/) { -- $self->log_info(" - will install all scripts\n"); -- $self->notes(chosen_scripts => 'all'); -- } -- elsif ($prompt =~ /^[iI]/) { -- $self->log_info(" - will install interactively:\n"); -- -- my @chosen_scripts; -- foreach my $group_dir (@group_dirs) { -- my $group = File::Basename::basename($group_dir); -- print " * group '$group' has:\n"; -- -- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; -- foreach my $script_file (@script_files) { -- my $script = File::Basename::basename($script_file); -- print " $script\n"; -- } -- -- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); -- die if $result =~ /^[qQ]/; -- if ($result =~ /^[yY]/) { -- $self->log_info(" + will install group '$group'\n"); -- push(@chosen_scripts, @script_files); -- } -- else { -- $self->log_info(" - will not install group '$group'\n"); -- } -- } - -- my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; -- -- $self->notes(chosen_scripts => $chosen_scripts); -- } -- else { -- $self->log_info(" - won't install any scripts\n"); -- $self->notes(chosen_scripts => 'none'); -- } -+ $self->log_info(" - willt install all scripts\n"); -+ $self->notes(chosen_scripts => 'all'); - - print "\n"; - } -@@ -1153,22 +1113,9 @@ - sub prompt_for_network { - my ($self, $accept) = @_; - -- my $proceed = $accept ? 0 : $self->y_n( "Do you want to run tests that require connection to servers across the internet\n" -- . "(likely to cause some failures)? y/n", 'n'); -- -- if ($proceed) { -- $self->notes('network' => 1); -- $self->log_info(" - will run internet-requiring tests\n"); -- my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n'); -- if ($use_email) { -- my $address = $self->prompt("Enter email address:"); -- $self->notes(email => $address); -- } -- } -- else { -- $self->notes(network => 0); -- $self->log_info(" - will not run internet-requiring tests\n"); -- } -+ my $proceed = 0; -+ $self->notes(network => 0); -+ $self->log_info(" - will not run internet-requiring tests\n"); - } - - =head2 print_build_script Property changes on: head/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-BioPerl/files/patch-Build.PL =================================================================== --- head/biology/p5-BioPerl/files/patch-Build.PL (revision 493446) +++ head/biology/p5-BioPerl/files/patch-Build.PL (nonexistent) @@ -1,114 +0,0 @@ ---- Build.PL.orig 2016-11-06 03:59:41 UTC -+++ Build.PL -@@ -226,7 +226,6 @@ my $build = Bio::Root::Build->new( - - build_requires => { - 'Module::Build' => 0.42, -- 'CPAN' => 1.81, - 'Test::Harness' => 2.62, - 'Test::Most' => 0, - 'URI::Escape' => 0 -@@ -413,101 +412,8 @@ sub test_biodbgff { - - sub prompt_for_biodb { - my $accept = shift; -- my $proceed = $accept ? 0 : $build->y_n( -- "Do you want to run the Bio::DB::GFF or " -- . "Bio::DB::SeqFeature::Store live database tests? " . "y/n", -- 'n' -- ); -- -- if ($proceed) { -- my @driver_choices; -- foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) { -- if ( grep {/$poss/i} @drivers ) { -- my $choice = $poss; -- $choice =~ s/^(.)/[$1]/; -- push( @driver_choices, $choice ); -- } -- } -- -- my $driver; -- if ( @driver_choices > 1 ) { -- my ($default) = $driver_choices[0] =~ /\[(.)/; -- $driver = $build->prompt( -- "Which database driver should be used? " -- . join( " ", @driver_choices ), -- $default -- ); -- } else { -- ($driver) = $driver_choices[0] =~ /\[(.)/; -- } -- if ( $driver =~ /^[mM]/ ) { -- $driver = 'mysql'; -- } elsif ( $driver =~ /^[pP]/ ) { -- $driver = 'Pg'; -- } elsif ( $driver =~ /^[oO]/ ) { -- $driver = 'Oracle'; -- } elsif ( $driver =~ /^[sS]/ ) { -- $driver = 'SQLite'; -- } -- -- my $test_db = $build->prompt( -- "Which database should I use for testing the $driver driver?\n" -- . "This database should already be present but doesn't have to " -- . "be preloaded for any schema", -- 'test' -- ); -- my $test_host = $build->prompt( -- "On which host is database '$test_db' running (hostname, ip address or host:port)", -- 'localhost' -- ); -- my $test_user = $build->prompt( -- "User name for connecting to database '$test_db'?", 'undef' ); -- my $test_pass = $build->prompt( -- "Password for connecting to database '$test_db'?", 'undef' ); -- -- my $use_host = 1; -- if ( $test_host eq 'undef' || $test_host eq 'localhost' ) { -- $use_host = 0; -- } -- -- my $test_dsn; -- if ( $driver eq 'Pg' || $driver eq 'SQLite' ) { -- $test_dsn = "dbi:$driver:dbname=$test_db"; -- $mysql_ok = 0; -- } else { -- $test_dsn = "dbi:$driver:database=$test_db"; -- $mysql_ok = 0; -- } -- if ($use_host) { -- $test_dsn .= ";host=$test_host"; -- } -- -- $build->notes( dbd_driver => $driver ); -- $build->notes( test_db => $test_db ); -- $build->notes( test_host => $test_host ); -- $build->notes( -- test_user => $test_user eq 'undef' ? undef : $test_user ); -- $build->notes( -- test_pass => $test_pass eq 'undef' ? undef : $test_pass ); -- $build->notes( test_dsn => $test_dsn ); -- -- $build->log_info( -- " - will run tests with database driver '$driver' and these settings:\n", -- " Database $test_db\n", -- " Host $test_host\n", -- " DSN $test_dsn\n", -- " User $test_user\n", -- " Password $test_pass\n" -- ); -- $build->log_info( " - will not run the BioDBSeqFeature live " -- . "database tests (requires MySQL or Pg driver)\n" ) -- unless ( $driver eq 'mysql' or $driver eq 'Pg' ); -- } else { -- $build->log_info( -- " - will not run the BioDBGFF or BioDBSeqFeature live database tests\n" -- ); -- } -- -+ my $proceed = 0; -+ $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); - $build->log_info("\n"); - return $proceed; - } Property changes on: head/biology/p5-BioPerl/files/patch-Build.PL ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/p5-BioPerl/Makefile =================================================================== --- head/biology/p5-BioPerl/Makefile (revision 493446) +++ head/biology/p5-BioPerl/Makefile (revision 493447) @@ -1,95 +1,77 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= BioPerl -PORTVERSION= 1.007002 +PORTVERSION= 1.007004 CATEGORIES= biology perl5 MASTER_SITES= CPAN -MASTER_SITE_SUBDIR= CPAN:CJFIELDS +MASTER_SITE_SUBDIR= CPAN:CDRAUG PKGNAMEPREFIX= p5- +DISTNAME= ${PORTNAME}-1.7.4 -MAINTAINER= perl@FreeBSD.org +MAINTAINER= sunpoet@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics LICENSE= ART10 GPLv1+ LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${RUN_DEPENDS} -RUN_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \ - p5-Array-Compare>=0:misc/p5-Array-Compare \ - p5-CGI>=0:www/p5-CGI \ - p5-Clone>=0:devel/p5-Clone \ - p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \ - p5-DBD-mysql>=0:databases/p5-DBD-mysql \ - p5-DBI>=0:databases/p5-DBI \ - p5-Data-Stag>=0.11:devel/p5-Data-Stag \ +RUN_DEPENDS= p5-DBI>=0:databases/p5-DBI \ + p5-Data-Stag>=0:devel/p5-Data-Stag \ p5-Error>=0:lang/p5-Error \ p5-GD>=0:graphics/p5-GD \ - p5-Graph>=0.50:math/p5-Graph \ - p5-GraphViz>=0:graphics/p5-GraphViz \ - p5-HTML-Parser>=3:www/p5-HTML-Parser \ - p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \ + p5-Graph>=0:math/p5-Graph \ p5-HTTP-Message>=0:www/p5-HTTP-Message \ p5-IO-String>=0:devel/p5-IO-String \ p5-IO-stringy>=0:devel/p5-IO-stringy \ - p5-Inline-C>=0.67:devel/p5-Inline-C \ + p5-IPC-Run>=0:devel/p5-IPC-Run \ p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ - p5-PostScript>=0:print/p5-PostScript \ - p5-SVG>=2.26:textproc/p5-SVG \ - p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \ + p5-Module-Build>=0:devel/p5-Module-Build \ p5-Set-Scalar>=0:devel/p5-Set-Scalar \ - p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \ - p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \ - p5-XML-DOM>=0:textproc/p5-XML-DOM \ + p5-Test-Most>=0:devel/p5-Test-Most \ + p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet \ + p5-URI>=0:net/p5-URI \ p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \ + p5-XML-DOM>=0:textproc/p5-XML-DOM \ p5-XML-LibXML>=0:textproc/p5-XML-LibXML \ - p5-XML-Parser>=0:textproc/p5-XML-Parser \ - p5-XML-SAX>=0.15:textproc/p5-XML-SAX \ + p5-XML-SAX-Base>=0:textproc/p5-XML-SAX-Base \ p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \ - p5-XML-Simple>=0:textproc/p5-XML-Simple \ + p5-XML-SAX>=0:textproc/p5-XML-SAX \ p5-XML-Twig>=0:textproc/p5-XML-Twig \ - p5-XML-Writer>=0.400:textproc/p5-XML-Writer \ + p5-XML-Writer>=0:textproc/p5-XML-Writer \ p5-YAML>=0:textproc/p5-YAML \ p5-libwww>=0:www/p5-libwww \ p5-libxml>=0:textproc/p5-libxml -TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \ - p5-URI>=0:net/p5-URI +TEST_DEPENDS= p5-Test-Memory-Cycle>=0:devel/p5-Test-Memory-Cycle \ + p5-Test-Weaken>=0:devel/p5-Test-Weaken USES= perl5 shebangfix -USE_PERL5= modbuild +USE_PERL5= configure + NO_ARCH= yes -SHEBANG_FILES= scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl -PORTDATA= * -PORTDOCS= * -PORTEXAMPLES= * - OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL -SQLITETEST_DESC= Test SQLite +SQLITETEST_DESC=Test SQLite + PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite -post-patch: - @${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \ - -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ - '1s|(/usr)?/bin/perl|${PERL}|' +SHEBANG_FILES= examples/*.pl examples/*/*.pl post-install: @${MKDIR} ${STAGEDIR}${DATADIR} - ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} + cd ${WRKSRC}/models && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md - ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} -.endfor - ${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes MANIFEST README.md ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} + cd ${WRKSRC}/examples/ && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include Index: head/biology/p5-BioPerl/distinfo =================================================================== --- head/biology/p5-BioPerl/distinfo (revision 493446) +++ head/biology/p5-BioPerl/distinfo (revision 493447) @@ -1,3 +1,3 @@ -TIMESTAMP = 1505232617 -SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1 -SIZE (BioPerl-1.007002.tar.gz) = 12362741 +TIMESTAMP = 1549651825 +SHA256 (BioPerl-1.7.4.tar.gz) = 5a074947bba299cdb47cbf1c66689502db02c022fc138459e3393da45d7c707b +SIZE (BioPerl-1.7.4.tar.gz) = 7642013 Index: head/biology/p5-BioPerl/pkg-plist =================================================================== --- head/biology/p5-BioPerl/pkg-plist (revision 493446) +++ head/biology/p5-BioPerl/pkg-plist (revision 493447) @@ -1,1702 +1,1105 @@ -bin/bp_aacomp.pl -bin/bp_biofetch_genbank_proxy.pl -bin/bp_bioflat_index.pl -bin/bp_biogetseq.pl -bin/bp_blast2tree.pl -bin/bp_bulk_load_gff.pl -bin/bp_chaos_plot.pl -bin/bp_classify_hits_kingdom.pl -bin/bp_composite_LD.pl -bin/bp_das_server.pl -bin/bp_dbsplit.pl -bin/bp_download_query_genbank.pl -bin/bp_extract_feature_seq.pl -bin/bp_fast_load_gff.pl -bin/bp_fastam9_to_table.pl -bin/bp_fetch.pl -bin/bp_filter_search.pl -bin/bp_find-blast-matches.pl -bin/bp_flanks.pl -bin/bp_gccalc.pl -bin/bp_genbank2gff.pl -bin/bp_genbank2gff3.pl -bin/bp_generate_histogram.pl -bin/bp_heterogeneity_test.pl -bin/bp_hivq.pl -bin/bp_hmmer_to_table.pl -bin/bp_index.pl -bin/bp_load_gff.pl -bin/bp_local_taxonomydb_query.pl -bin/bp_make_mrna_protein.pl -bin/bp_mask_by_search.pl -bin/bp_meta_gff.pl -bin/bp_mrtrans.pl -bin/bp_mutate.pl -bin/bp_netinstall.pl -bin/bp_nexus2nh.pl -bin/bp_nrdb.pl -bin/bp_oligo_count.pl -bin/bp_parse_hmmsearch.pl -bin/bp_process_gadfly.pl -bin/bp_process_sgd.pl -bin/bp_process_wormbase.pl -bin/bp_query_entrez_taxa.pl -bin/bp_remote_blast.pl -bin/bp_revtrans-motif.pl -bin/bp_search2alnblocks.pl -bin/bp_search2gff.pl -bin/bp_search2table.pl -bin/bp_search2tribe.pl -bin/bp_seq_length.pl -bin/bp_seqconvert.pl -bin/bp_seqcut.pl -bin/bp_seqfeature_delete.pl -bin/bp_seqfeature_gff3.pl -bin/bp_seqfeature_load.pl -bin/bp_seqpart.pl -bin/bp_seqret.pl -bin/bp_seqretsplit.pl -bin/bp_split_seq.pl -bin/bp_sreformat.pl -bin/bp_taxid4species.pl -bin/bp_taxonomy2tree.pl -bin/bp_translate_seq.pl -bin/bp_tree2pag.pl -bin/bp_unflatten_seq.pl +bin/bp_aacomp +bin/bp_bioflat_index +bin/bp_biogetseq +bin/bp_chaos_plot +bin/bp_classify_hits_kingdom +bin/bp_dbsplit +bin/bp_extract_feature_seq +bin/bp_fastam9_to_table +bin/bp_fetch +bin/bp_filter_search +bin/bp_find-blast-matches +bin/bp_gccalc +bin/bp_genbank2gff3 +bin/bp_index +bin/bp_local_taxonomydb_query +bin/bp_make_mrna_protein +bin/bp_mask_by_search +bin/bp_mrtrans +bin/bp_mutate +bin/bp_nexus2nh +bin/bp_nrdb +bin/bp_oligo_count +bin/bp_process_gadfly +bin/bp_process_sgd +bin/bp_revtrans-motif +bin/bp_search2alnblocks +bin/bp_search2gff +bin/bp_search2table +bin/bp_search2tribe +bin/bp_seq_length +bin/bp_seqconvert +bin/bp_seqcut +bin/bp_seqpart +bin/bp_seqret +bin/bp_seqretsplit +bin/bp_split_seq +bin/bp_sreformat +bin/bp_taxid4species +bin/bp_taxonomy2tree +bin/bp_translate_seq +bin/bp_tree2pag +bin/bp_unflatten_seq %%SITE_PERL%%/Bio/Align/AlignI.pm %%SITE_PERL%%/Bio/Align/DNAStatistics.pm -%%SITE_PERL%%/Bio/Align/Graphics.pm %%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm %%SITE_PERL%%/Bio/Align/ProteinStatistics.pm %%SITE_PERL%%/Bio/Align/StatisticsI.pm %%SITE_PERL%%/Bio/Align/Utilities.pm %%SITE_PERL%%/Bio/AlignIO.pm %%SITE_PERL%%/Bio/AlignIO/Handler/GenericAlignHandler.pm %%SITE_PERL%%/Bio/AlignIO/arp.pm %%SITE_PERL%%/Bio/AlignIO/bl2seq.pm %%SITE_PERL%%/Bio/AlignIO/clustalw.pm %%SITE_PERL%%/Bio/AlignIO/emboss.pm %%SITE_PERL%%/Bio/AlignIO/fasta.pm %%SITE_PERL%%/Bio/AlignIO/largemultifasta.pm %%SITE_PERL%%/Bio/AlignIO/maf.pm %%SITE_PERL%%/Bio/AlignIO/mase.pm %%SITE_PERL%%/Bio/AlignIO/mega.pm %%SITE_PERL%%/Bio/AlignIO/meme.pm %%SITE_PERL%%/Bio/AlignIO/metafasta.pm %%SITE_PERL%%/Bio/AlignIO/msf.pm -%%SITE_PERL%%/Bio/AlignIO/nexml.pm %%SITE_PERL%%/Bio/AlignIO/nexus.pm %%SITE_PERL%%/Bio/AlignIO/pfam.pm %%SITE_PERL%%/Bio/AlignIO/phylip.pm %%SITE_PERL%%/Bio/AlignIO/po.pm %%SITE_PERL%%/Bio/AlignIO/proda.pm %%SITE_PERL%%/Bio/AlignIO/prodom.pm %%SITE_PERL%%/Bio/AlignIO/psi.pm %%SITE_PERL%%/Bio/AlignIO/selex.pm -%%SITE_PERL%%/Bio/AlignIO/stockholm.pm %%SITE_PERL%%/Bio/AlignIO/xmfa.pm %%SITE_PERL%%/Bio/AnalysisI.pm %%SITE_PERL%%/Bio/AnalysisParserI.pm %%SITE_PERL%%/Bio/AnalysisResultI.pm %%SITE_PERL%%/Bio/AnnotatableI.pm %%SITE_PERL%%/Bio/Annotation/AnnotationFactory.pm %%SITE_PERL%%/Bio/Annotation/Collection.pm %%SITE_PERL%%/Bio/Annotation/Comment.pm %%SITE_PERL%%/Bio/Annotation/DBLink.pm %%SITE_PERL%%/Bio/Annotation/OntologyTerm.pm %%SITE_PERL%%/Bio/Annotation/Reference.pm %%SITE_PERL%%/Bio/Annotation/Relation.pm %%SITE_PERL%%/Bio/Annotation/SimpleValue.pm %%SITE_PERL%%/Bio/Annotation/StructuredValue.pm %%SITE_PERL%%/Bio/Annotation/TagTree.pm %%SITE_PERL%%/Bio/Annotation/Target.pm %%SITE_PERL%%/Bio/Annotation/Tree.pm %%SITE_PERL%%/Bio/Annotation/TypeManager.pm %%SITE_PERL%%/Bio/AnnotationCollectionI.pm %%SITE_PERL%%/Bio/AnnotationI.pm -%%SITE_PERL%%/Bio/Assembly/Contig.pm -%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm -%%SITE_PERL%%/Bio/Assembly/IO.pm -%%SITE_PERL%%/Bio/Assembly/IO/ace.pm -%%SITE_PERL%%/Bio/Assembly/IO/bowtie.pm -%%SITE_PERL%%/Bio/Assembly/IO/maq.pm -%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm -%%SITE_PERL%%/Bio/Assembly/IO/sam.pm -%%SITE_PERL%%/Bio/Assembly/IO/tigr.pm -%%SITE_PERL%%/Bio/Assembly/Scaffold.pm -%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm -%%SITE_PERL%%/Bio/Assembly/Singlet.pm 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