FreeBSD Bugzilla – Attachment 190502 Details for
Bug 225682
[maintainer-update] biology/seqan and biology/seqan-apps
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[patch]
Updated patch: biology/seqan
seqan.patch (text/plain), 90.00 KB, created by
Yuri Victorovich
on 2018-02-11 10:23:58 UTC
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Description:
Updated patch: biology/seqan
Filename:
MIME Type:
Creator:
Yuri Victorovich
Created:
2018-02-11 10:23:58 UTC
Size:
90.00 KB
patch
obsolete
>Index: biology/seqan/Makefile >=================================================================== >--- biology/seqan/Makefile (revision 461453) >+++ biology/seqan/Makefile (working copy) >@@ -2,13 +2,13 @@ > # $FreeBSD$ > > PORTNAME= seqan >-PORTVERSION= 2.2.0 >+DISTVERSION= 2.4.0 > CATEGORIES= biology > MASTER_SITES= http://packages.seqan.de/seqan-library/ > DISTNAME= ${PORTNAME}-library-${PORTVERSION} > > MAINTAINER= h2+fbsdports@fsfe.org >-COMMENT= C++ Sequence Analysis Template Library >+COMMENT= C++ sequence analysis template library > > LICENSE= BSD3CLAUSE > LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE >@@ -15,17 +15,22 @@ > > USES= tar:xz > NO_BUILD= yes >+NO_ARCH= yes > > CONFLICTS= seqan1-[0-9]* > > OPTIONS_DEFINE= DOCS >-DOCS_DESC= Install official API documentation (html) > >+PORTDOCS= * >+ >+post-patch: # delete empty doc dirs >+ @cd ${WRKSRC}/share/doc/seqan/html && ${RMDIR} docs/seqan docs lists >+ > do-install: > cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include >- ${MKDIR} ${STAGEDIR}/${PREFIX}/share/cmake/Modules >- ${INSTALL_DATA} ${WRKSRC}/share/cmake/Modules/FindSeqAn.cmake ${STAGEDIR}/${PREFIX}/share/cmake/Modules/ >- ${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig >+ @${MKDIR} ${STAGEDIR}/${PREFIX}/lib/cmake/seqan >+ ${INSTALL_DATA} ${WRKSRC}/share/cmake/seqan/seqan-config.cmake ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/ >+ @${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig > ${INSTALL_DATA} ${WRKSRC}/share/pkgconfig/seqan-2.pc ${STAGEDIR}/${PREFIX}/libdata/pkgconfig/ > > do-install-DOCS-on: >Index: biology/seqan/distinfo >=================================================================== >--- biology/seqan/distinfo (revision 461453) >+++ biology/seqan/distinfo (working copy) >@@ -1,3 +1,3 @@ >-TIMESTAMP = 1473846790 >-SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd >-SIZE (seqan-library-2.2.0.tar.xz) = 5223004 >+TIMESTAMP = 1517832492 >+SHA256 (seqan-library-2.4.0.tar.xz) = dd97b1514ab83acb7d7be911b157979e188e8ca72cc61c430c1e0fd03bcd41a5 >+SIZE (seqan-library-2.4.0.tar.xz) = 4868868 >Index: biology/seqan/pkg-descr >=================================================================== >--- biology/seqan/pkg-descr (revision 461453) >+++ biology/seqan/pkg-descr (working copy) >@@ -3,7 +3,7 @@ > focus on biological data. The library is licensed under the > 3-clause BSD license except the applications which are GPL. > >-This port now only contains the header library and API >-documentation. The apps are separate. >+This port only contains the header library and API documentation. >+The apps are installed by biology/seqan-apps. > >-WWW: http://www.seqan.de/ >+WWW: http://www.seqan.de >Index: biology/seqan/pkg-plist >=================================================================== >--- biology/seqan/pkg-plist (revision 461453) >+++ biology/seqan/pkg-plist (working copy) >@@ -6,6 +6,7 @@ > include/seqan/align/align_iterator_base.h > include/seqan/align/align_metafunctions.h > include/seqan/align/align_traceback.h >+include/seqan/align/aligned_sequence_concept.h > include/seqan/align/alignment_algorithm_tags.h > include/seqan/align/alignment_operations.h > include/seqan/align/dp_algorithm_impl.h >@@ -62,6 +63,26 @@ > include/seqan/align_extend/align_extend.h > include/seqan/align_extend/align_extend_base.h > include/seqan/align_extend/dp_scout_xdrop.h >+include/seqan/align_parallel.h >+include/seqan/align_parallel/async_wave_execution_interface.h >+include/seqan/align_parallel/dp_kernel_adaptor.h >+include/seqan/align_parallel/dp_parallel_execution_policies.h >+include/seqan/align_parallel/dp_parallel_scout.h >+include/seqan/align_parallel/dp_parallel_scout_simd.h >+include/seqan/align_parallel/dp_settings.h >+include/seqan/align_parallel/dp_traits.h >+include/seqan/align_parallel/parallel_align_interface.h >+include/seqan/align_parallel/wavefront_alignment_executor.h >+include/seqan/align_parallel/wavefront_alignment_result.h >+include/seqan/align_parallel/wavefront_alignment_scheduler.h >+include/seqan/align_parallel/wavefront_alignment_task.h >+include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h >+include/seqan/align_parallel/wavefront_task.h >+include/seqan/align_parallel/wavefront_task_event.h >+include/seqan/align_parallel/wavefront_task_executor.h >+include/seqan/align_parallel/wavefront_task_queue.h >+include/seqan/align_parallel/wavefront_task_scheduler.h >+include/seqan/align_parallel/wavefront_task_util.h > include/seqan/align_profile.h > include/seqan/align_profile/add_to_profile.h > include/seqan/align_profile/score_profile_seq.h >@@ -84,6 +105,7 @@ > include/seqan/arg_parse/arg_parse_option.h > include/seqan/arg_parse/arg_parse_parse.h > include/seqan/arg_parse/arg_parse_type_support.h >+include/seqan/arg_parse/arg_parse_version_check.h > include/seqan/arg_parse/argument_parser.h > include/seqan/arg_parse/tool_doc.h > include/seqan/arg_parse/xml_support.h >@@ -137,7 +159,6 @@ > include/seqan/basic/basic_metaprogramming.h > include/seqan/basic/basic_parallelism.h > include/seqan/basic/basic_proxy.h >-include/seqan/basic/basic_simd_vector.h > include/seqan/basic/basic_smart_pointer.h > include/seqan/basic/basic_stream.h > include/seqan/basic/basic_tangle.h >@@ -267,6 +288,7 @@ > include/seqan/graph_algorithms/graph_algorithm_hmm.h > include/seqan/graph_algorithms/graph_algorithm_lis_his.h > include/seqan/graph_algorithms/kruskal.h >+include/seqan/graph_algorithms/maximum_weighted_matching.h > include/seqan/graph_algorithms/path_growing.h > include/seqan/graph_algorithms/prim.h > include/seqan/graph_algorithms/single_source_shortest_path.h >@@ -326,6 +348,7 @@ > include/seqan/index/find2_base.h > include/seqan/index/find2_functors.h > include/seqan/index/find2_index.h >+include/seqan/index/find2_index_approx.h > include/seqan/index/find2_index_multi.h > include/seqan/index/find2_vstree_factory.h > include/seqan/index/find_backtracking.h >@@ -476,6 +499,8 @@ > include/seqan/modifier/modifier_string.h > include/seqan/modifier/modifier_view.h > include/seqan/parallel.h >+include/seqan/parallel/enumerable_thread_local.h >+include/seqan/parallel/enumerable_thread_local_iterator.h > include/seqan/parallel/parallel_algorithms.h > include/seqan/parallel/parallel_atomic_misc.h > include/seqan/parallel/parallel_atomic_primitives.h >@@ -488,6 +513,7 @@ > include/seqan/parallel/parallel_serializer.h > include/seqan/parallel/parallel_splitting.h > include/seqan/parallel/parallel_tags.h >+include/seqan/parallel/parallel_thread_pool.h > include/seqan/parse_lm.h > include/seqan/parse_lm/local_match_store.h > include/seqan/parse_lm/parse_blastn_tabular.h >@@ -521,12 +547,33 @@ > include/seqan/reduced_aminoacid.h > include/seqan/reduced_aminoacid/reduced_aminoacid_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_li10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h > include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h >+include/seqan/rna_io.h >+include/seqan/rna_io/bpseq_read_write.h >+include/seqan/rna_io/connect_read_write.h >+include/seqan/rna_io/dot_bracket_read_write.h >+include/seqan/rna_io/ebpseq_read_write.h >+include/seqan/rna_io/rna_header.h >+include/seqan/rna_io/rna_io_context.h >+include/seqan/rna_io/rna_record.h >+include/seqan/rna_io/rna_struct_file.h >+include/seqan/rna_io/stockholm_read_write.h >+include/seqan/rna_io/vienna_read_write.h > include/seqan/roi_io.h > include/seqan/roi_io/read_roi.h > include/seqan/roi_io/roi_file.h >@@ -564,6 +611,7 @@ > include/seqan/seeds/seeds_seed_set_unordered.h > include/seqan/seeds/seeds_seed_simple.h > include/seqan/seq_io.h >+include/seqan/seq_io/bam_sam.h > include/seqan/seq_io/fai_index.h > include/seqan/seq_io/fasta_fastq.h > include/seqan/seq_io/genomic_region.h >@@ -606,6 +654,14 @@ > include/seqan/sequence_journaled/sequence_journaled.h > include/seqan/sequence_journaled/sequence_journaled_iterator.h > include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h >+include/seqan/simd.h >+include/seqan/simd/simd_base.h >+include/seqan/simd/simd_base_seqan_impl.h >+include/seqan/simd/simd_base_seqan_impl_avx2.h >+include/seqan/simd/simd_base_seqan_impl_avx512.h >+include/seqan/simd/simd_base_seqan_impl_sse4.2.h >+include/seqan/simd/simd_base_seqan_interface.h >+include/seqan/simd/simd_base_umesimd_impl.h > include/seqan/simple_intervals_io.h > include/seqan/simple_intervals_io/simple_intervals_file.h > include/seqan/simple_intervals_io/simple_intervals_io.h >@@ -671,1243 +727,5 @@ > include/seqan/vcf_io/vcf_record.h > include/seqan/vcf_io/write_vcf.h > include/seqan/version.h >+lib/cmake/seqan/seqan-config.cmake > libdata/pkgconfig/seqan-2.pc >-share/cmake/Modules/FindSeqAn.cmake >-%%PORTDOCS%%%%DOCSDIR%%/CHANGELOG.rst >-%%PORTDOCS%%%%DOCSDIR%%/LICENSE >-%%PORTDOCS%%%%DOCSDIR%%/README.rst >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AFScore.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_Accumulator.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_Align.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignCols.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignConfig.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignQualityStoreElement.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignTraceback.html >-%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignedReadLayout.html 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