Index: head/biology/p5-BioPerl/Makefile =================================================================== --- head/biology/p5-BioPerl/Makefile (revision 449745) +++ head/biology/p5-BioPerl/Makefile (revision 449746) @@ -1,96 +1,95 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= BioPerl -PORTVERSION= 1.007001 -PORTREVISION= 2 +PORTVERSION= 1.007002 CATEGORIES= biology perl5 MASTER_SITES= CPAN MASTER_SITE_SUBDIR= CPAN:CJFIELDS PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics LICENSE= ART10 GPLv1 LICENSE_COMB= dual BUILD_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 \ 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-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-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-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-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \ 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-Writer>=0:textproc/p5-XML-SAX-Writer \ p5-XML-Simple>=0:textproc/p5-XML-Simple \ p5-XML-Twig>=0:textproc/p5-XML-Twig \ p5-XML-Writer>=0.400:textproc/p5-XML-Writer \ p5-YAML>=0:textproc/p5-YAML \ p5-libwww>=0:www/p5-libwww \ p5-libxml>=0:textproc/p5-libxml RUN_DEPENDS:= ${BUILD_DEPENDS} TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \ p5-URI>=0:net/p5-URI USES= perl5 shebangfix USE_PERL5= modbuild NO_ARCH= yes SHEBANG_FILES= scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl PORTDATA= * PORTDOCS= * PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL SQLITETEST_DESC= Test SQLite PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:databases/p5-DBD-SQLite post-patch: @${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \ -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ '1s|(/usr)?/bin/perl|${PERL}|' post-install: @${MKDIR} ${STAGEDIR}${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${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} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} .include Index: head/biology/p5-BioPerl/distinfo =================================================================== --- head/biology/p5-BioPerl/distinfo (revision 449745) +++ head/biology/p5-BioPerl/distinfo (revision 449746) @@ -1,3 +1,3 @@ -TIMESTAMP = 1479828383 -SHA256 (BioPerl-1.007001.tar.gz) = 9da1dbcd10452f53194c98c6cc2f604a59124507dcc1e6a8440565f44dd07b40 -SIZE (BioPerl-1.007001.tar.gz) = 12486953 +TIMESTAMP = 1505232617 +SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1 +SIZE (BioPerl-1.007002.tar.gz) = 12362741 Index: head/biology/p5-BioPerl/pkg-plist =================================================================== --- head/biology/p5-BioPerl/pkg-plist (revision 449745) +++ head/biology/p5-BioPerl/pkg-plist (revision 449746) @@ -1,1712 +1,1702 @@ 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_pairwise_kaks.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 %%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 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%%SITE_PERL%%/Bio/DB/FileCache.pm %%SITE_PERL%%/Bio/DB/Flat.pm %%SITE_PERL%%/Bio/DB/Flat/BDB.pm %%SITE_PERL%%/Bio/DB/Flat/BDB/embl.pm %%SITE_PERL%%/Bio/DB/Flat/BDB/fasta.pm %%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm %%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm %%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm %%SITE_PERL%%/Bio/DB/GFF.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/ace.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch_oracle.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysql.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracle.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracleace.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/iterator.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/alignment.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/clone.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/coding.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/gene.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/orf.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/processed_transcript.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/so_transcript.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/transcript.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_acembly.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_genscan.pm %%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_refgene.pm 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