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Sun, 5 May 2024 11:35:57 GMT (envelope-from git) Date: Sun, 5 May 2024 11:35:57 GMT Message-Id: <202405051135.445BZvWU008273@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Rene Ladan Subject: git: 2248d57ea52e - main - biology/pbseqan: Remove expired port List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: rene X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 2248d57ea52e5abb1f610e245f19b31edea0bdbd Auto-Submitted: auto-generated The branch main has been updated by rene: URL: https://cgit.FreeBSD.org/ports/commit/?id=2248d57ea52e5abb1f610e245f19b31edea0bdbd commit 2248d57ea52e5abb1f610e245f19b31edea0bdbd Author: Rene Ladan AuthorDate: 2024-05-05 11:35:30 +0000 Commit: Rene Ladan CommitDate: 2024-05-05 11:35:44 +0000 biology/pbseqan: Remove expired port 2024-05-05 biology/pbseqan: Upstream merged into SeqAn project: Use biology/seqan --- MOVED | 1 + biology/Makefile | 1 - biology/pbseqan/Makefile | 30 --- biology/pbseqan/distinfo | 3 - biology/pbseqan/pkg-descr | 9 - biology/pbseqan/pkg-plist | 657 ---------------------------------------------- 6 files changed, 1 insertion(+), 700 deletions(-) diff --git a/MOVED b/MOVED index 400702abdf82..2ee88ca75019 100644 --- a/MOVED +++ b/MOVED @@ -3232,3 +3232,4 @@ lang/gcc48||2024-05-01|Has expired: Unsupported by upstream since 2015. Use GCC multimedia/rubygem-paperclip-av-transcoder-rails50||2024-05-04|Has expired: Depends on deprecated port devel/rubygem-paperclip-rails50 devel/rubygem-paperclip-rails50||2024-05-04|Has expired: Upstream repo archived Jul 13, 2023. Upstream recommends using Rails' own ActiveStorage devel/rubygem-paperclip-rails5||2024-05-04|Has expired: Upstream repo archived Jul 13, 2023. Upstream recommends using Rails' own ActiveStorage +biology/pbseqan|biology/seqan|2024-05-05|Has expired: Upstream merged into SeqAn project: Use biology/seqan diff --git a/biology/Makefile b/biology/Makefile index 742a6885b0d2..2a6da67d4b30 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -142,7 +142,6 @@ SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam - SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap diff --git a/biology/pbseqan/Makefile b/biology/pbseqan/Makefile deleted file mode 100644 index a7d8d6e04759..000000000000 --- a/biology/pbseqan/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -PORTNAME= pbseqan -DISTVERSION= g20171011 -CATEGORIES= biology - -# As of March 2018, unanimity is no longer open source. -# See https://github.com/PacificBiosciences/ccs. -MAINTAINER= ports@FreeBSD.org -COMMENT= Pacific Biosciences patched and stripped down SeqAn -WWW= https://github.com/PacificBiosciences/seqan - -LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Upstream merged into SeqAn project: Use biology/seqan -EXPIRATION_DATE= 2024-05-05 - -USE_GITHUB= yes -GH_ACCOUNT= PacificBiosciences -GH_PROJECT= seqan -GH_TAGNAME= 21d95d737d8decb5cc3693b9065d81e831e7f57d - -NO_BUILD= yes -NO_ARCH= yes - -do-install: - @${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio - cd ${WRKSRC}/include/seqan && \ - ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include/PacBio/seqan - -.include diff --git a/biology/pbseqan/distinfo b/biology/pbseqan/distinfo deleted file mode 100644 index ac3b9e5292f5..000000000000 --- a/biology/pbseqan/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1550366556 -SHA256 (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = dcdc564c877190089bd691ab4097164266e675217645613426fb1ff44029da8c -SIZE (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = 1527033 diff --git a/biology/pbseqan/pkg-descr b/biology/pbseqan/pkg-descr deleted file mode 100644 index 40bf624533db..000000000000 --- a/biology/pbseqan/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -This is a public fork of the SeqAn Library v2.0.0, stripped down to just the -header files and with a few custom fixes. - -Some of PacBio's tools depend on SeqAn for efficient implementations of some -common data-structures for sequence analysis (A huge thanks to SeqAn -development team!). However PacBio only uses a small amount of the SeqAn -code-base, and in addition requires a few minor fixes that didn't make it in to -the initial release of SeqAn v2.0.0. Thus to minimize confusion and band-width, -we will depend on this fork instead of SeqAn proper. diff --git a/biology/pbseqan/pkg-plist b/biology/pbseqan/pkg-plist deleted file mode 100644 index a5019b19b101..000000000000 --- a/biology/pbseqan/pkg-plist +++ /dev/null @@ -1,657 +0,0 @@ -include/PacBio/seqan/LICENSE -include/PacBio/seqan/align.h -include/PacBio/seqan/align/align_base.h -include/PacBio/seqan/align/align_cols.h -include/PacBio/seqan/align/align_config.h -include/PacBio/seqan/align/align_iterator_base.h -include/PacBio/seqan/align/align_metafunctions.h -include/PacBio/seqan/align/align_traceback.h -include/PacBio/seqan/align/alignment_algorithm_tags.h -include/PacBio/seqan/align/alignment_operations.h -include/PacBio/seqan/align/dp_algorithm_impl.h -include/PacBio/seqan/align/dp_band.h -include/PacBio/seqan/align/dp_cell.h -include/PacBio/seqan/align/dp_cell_affine.h -include/PacBio/seqan/align/dp_cell_dynamic.h -include/PacBio/seqan/align/dp_cell_linear.h -include/PacBio/seqan/align/dp_context.h -include/PacBio/seqan/align/dp_formula.h -include/PacBio/seqan/align/dp_formula_affine.h -include/PacBio/seqan/align/dp_formula_dynamic.h -include/PacBio/seqan/align/dp_formula_linear.h -include/PacBio/seqan/align/dp_matrix.h -include/PacBio/seqan/align/dp_matrix_navigator.h -include/PacBio/seqan/align/dp_matrix_navigator_score_matrix.h -include/PacBio/seqan/align/dp_matrix_navigator_score_matrix_sparse.h -include/PacBio/seqan/align/dp_matrix_navigator_trace_matrix.h -include/PacBio/seqan/align/dp_matrix_sparse.h -include/PacBio/seqan/align/dp_meta_info.h -include/PacBio/seqan/align/dp_profile.h -include/PacBio/seqan/align/dp_scout.h -include/PacBio/seqan/align/dp_setup.h -include/PacBio/seqan/align/dp_trace_segment.h -include/PacBio/seqan/align/dp_traceback_adaptor.h -include/PacBio/seqan/align/dp_traceback_impl.h -include/PacBio/seqan/align/evaluate_alignment.h -include/PacBio/seqan/align/fragment.h -include/PacBio/seqan/align/gap_anchor.h -include/PacBio/seqan/align/gapped_value_type.h -include/PacBio/seqan/align/gaps_anchor.h -include/PacBio/seqan/align/gaps_array.h -include/PacBio/seqan/align/gaps_base.h -include/PacBio/seqan/align/gaps_iterator_anchor.h -include/PacBio/seqan/align/gaps_iterator_array.h -include/PacBio/seqan/align/gaps_iterator_base.h -include/PacBio/seqan/align/global_alignment_banded.h -include/PacBio/seqan/align/global_alignment_hirschberg_impl.h -include/PacBio/seqan/align/global_alignment_myers_hirschberg_impl.h -include/PacBio/seqan/align/global_alignment_myers_impl.h -include/PacBio/seqan/align/global_alignment_specialized.h -include/PacBio/seqan/align/global_alignment_unbanded.h -include/PacBio/seqan/align/local_alignment_banded.h -include/PacBio/seqan/align/local_alignment_banded_waterman_eggert_impl.h -include/PacBio/seqan/align/local_alignment_enumeration.h -include/PacBio/seqan/align/local_alignment_enumeration_banded.h -include/PacBio/seqan/align/local_alignment_enumeration_unbanded.h -include/PacBio/seqan/align/local_alignment_unbanded.h -include/PacBio/seqan/align/local_alignment_waterman_eggert_impl.h -include/PacBio/seqan/align/matrix_base.h -include/PacBio/seqan/align_extend.h -include/PacBio/seqan/align_extend/align_extend.h -include/PacBio/seqan/align_extend/align_extend_base.h -include/PacBio/seqan/align_extend/dp_scout_xdrop.h -include/PacBio/seqan/align_profile.h -include/PacBio/seqan/align_profile/add_to_profile.h -include/PacBio/seqan/align_profile/score_profile_seq.h -include/PacBio/seqan/align_split.h -include/PacBio/seqan/align_split/align_split_interface.h -include/PacBio/seqan/align_split/dp_scout_split.h -include/PacBio/seqan/alignment_free.h -include/PacBio/seqan/alignment_free/af_d2.h -include/PacBio/seqan/alignment_free/af_d2star.h -include/PacBio/seqan/alignment_free/af_d2z.h -include/PacBio/seqan/alignment_free/af_n2.h -include/PacBio/seqan/alignment_free/alignment_free_base.h -include/PacBio/seqan/alignment_free/alignment_free_comparison.h -include/PacBio/seqan/alignment_free/kmer_functions.h -include/PacBio/seqan/arg_parse.h -include/PacBio/seqan/arg_parse/arg_parse_argument.h -include/PacBio/seqan/arg_parse/arg_parse_ctd_support.h -include/PacBio/seqan/arg_parse/arg_parse_doc.h -include/PacBio/seqan/arg_parse/arg_parse_exceptions.h -include/PacBio/seqan/arg_parse/arg_parse_option.h -include/PacBio/seqan/arg_parse/arg_parse_parse.h -include/PacBio/seqan/arg_parse/arg_parse_type_support.h -include/PacBio/seqan/arg_parse/argument_parser.h -include/PacBio/seqan/arg_parse/tool_doc.h -include/PacBio/seqan/arg_parse/xml_support.h -include/PacBio/seqan/bam_io.h -include/PacBio/seqan/bam_io/bam_alignment_record.h -include/PacBio/seqan/bam_io/bam_alignment_record_util.h -include/PacBio/seqan/bam_io/bam_file.h -include/PacBio/seqan/bam_io/bam_header_record.h -include/PacBio/seqan/bam_io/bam_index_bai.h -include/PacBio/seqan/bam_io/bam_io_context.h -include/PacBio/seqan/bam_io/bam_sam_conversion.h -include/PacBio/seqan/bam_io/bam_scanner_cache.h -include/PacBio/seqan/bam_io/bam_tags_dict.h -include/PacBio/seqan/bam_io/cigar.h -include/PacBio/seqan/bam_io/read_bam.h -include/PacBio/seqan/bam_io/read_sam.h -include/PacBio/seqan/bam_io/write_bam.h -include/PacBio/seqan/bam_io/write_sam.h -include/PacBio/seqan/basic.h -include/PacBio/seqan/basic/aggregate_concept.h -include/PacBio/seqan/basic/allocator_chunkpool.h -include/PacBio/seqan/basic/allocator_interface.h -include/PacBio/seqan/basic/allocator_multipool.h -include/PacBio/seqan/basic/allocator_simple.h -include/PacBio/seqan/basic/allocator_singlepool.h -include/PacBio/seqan/basic/allocator_to_std.h -include/PacBio/seqan/basic/alphabet_adapt_builtins.h -include/PacBio/seqan/basic/alphabet_bio.h -include/PacBio/seqan/basic/alphabet_concept.h -include/PacBio/seqan/basic/alphabet_math.h -include/PacBio/seqan/basic/alphabet_profile.h -include/PacBio/seqan/basic/alphabet_qualities.h -include/PacBio/seqan/basic/alphabet_residue.h -include/PacBio/seqan/basic/alphabet_residue_funcs.h -include/PacBio/seqan/basic/alphabet_residue_tabs.h -include/PacBio/seqan/basic/alphabet_simple_type.h -include/PacBio/seqan/basic/alphabet_storage.h -include/PacBio/seqan/basic/array_construct_destruct.h -include/PacBio/seqan/basic/basic_aggregate.h -include/PacBio/seqan/basic/basic_allocator.h -include/PacBio/seqan/basic/basic_alphabet.h -include/PacBio/seqan/basic/basic_concept.h -include/PacBio/seqan/basic/basic_container.h -include/PacBio/seqan/basic/basic_debug.h -include/PacBio/seqan/basic/basic_device.h -include/PacBio/seqan/basic/basic_exception.h -include/PacBio/seqan/basic/basic_functors.h -include/PacBio/seqan/basic/basic_fundamental.h -include/PacBio/seqan/basic/basic_iterator.h -include/PacBio/seqan/basic/basic_math.h -include/PacBio/seqan/basic/basic_metaprogramming.h -include/PacBio/seqan/basic/basic_parallelism.h -include/PacBio/seqan/basic/basic_proxy.h -include/PacBio/seqan/basic/basic_simd_vector.h -include/PacBio/seqan/basic/basic_smart_pointer.h -include/PacBio/seqan/basic/basic_stream.h -include/PacBio/seqan/basic/basic_tangle.h -include/PacBio/seqan/basic/basic_type.h -include/PacBio/seqan/basic/basic_view.h -include/PacBio/seqan/basic/boost_preprocessor_subset.h -include/PacBio/seqan/basic/builtin_functions.h -include/PacBio/seqan/basic/concept_checking.h -include/PacBio/seqan/basic/container_concept.h -include/PacBio/seqan/basic/debug_helper.h -include/PacBio/seqan/basic/debug_test_system.h -include/PacBio/seqan/basic/fundamental_chunking.h -include/PacBio/seqan/basic/fundamental_comparison.h -include/PacBio/seqan/basic/fundamental_concepts.h -include/PacBio/seqan/basic/fundamental_conversion.h -include/PacBio/seqan/basic/fundamental_metafunctions.h -include/PacBio/seqan/basic/fundamental_tags.h -include/PacBio/seqan/basic/fundamental_transport.h -include/PacBio/seqan/basic/holder_base.h -include/PacBio/seqan/basic/holder_simple.h -include/PacBio/seqan/basic/holder_tristate.h -include/PacBio/seqan/basic/hosted_type_interface.h -include/PacBio/seqan/basic/iterator_adapt_pointer.h -include/PacBio/seqan/basic/iterator_adapt_std.h -include/PacBio/seqan/basic/iterator_adaptor.h -include/PacBio/seqan/basic/iterator_base.h -include/PacBio/seqan/basic/iterator_concept.h -include/PacBio/seqan/basic/iterator_counting.h -include/PacBio/seqan/basic/iterator_interface.h -include/PacBio/seqan/basic/iterator_position.h -include/PacBio/seqan/basic/iterator_range.h -include/PacBio/seqan/basic/macro_deprecated.h -include/PacBio/seqan/basic/math_functions.h -include/PacBio/seqan/basic/math_log_space_value.h -include/PacBio/seqan/basic/metaprogramming_control.h -include/PacBio/seqan/basic/metaprogramming_enable_if.h -include/PacBio/seqan/basic/metaprogramming_logic.h -include/PacBio/seqan/basic/metaprogramming_math.h -include/PacBio/seqan/basic/metaprogramming_type.h -include/PacBio/seqan/basic/metaprogramming_type_algebra.h -include/PacBio/seqan/basic/pair_base.h -include/PacBio/seqan/basic/pair_bit_compressed.h -include/PacBio/seqan/basic/pair_packed.h -include/PacBio/seqan/basic/profiling.h -include/PacBio/seqan/basic/property_map_concept.h -include/PacBio/seqan/basic/proxy_base.h -include/PacBio/seqan/basic/proxy_iterator.h -include/PacBio/seqan/basic/test_system.h -include/PacBio/seqan/basic/triple_base.h -include/PacBio/seqan/basic/triple_packed.h -include/PacBio/seqan/basic/tuple_base.h -include/PacBio/seqan/basic/tuple_bit_compressed.h -include/PacBio/seqan/basic/volatile_ptr.h -include/PacBio/seqan/bed_io.h -include/PacBio/seqan/bed_io/bed_file.h -include/PacBio/seqan/bed_io/bed_record.h -include/PacBio/seqan/bed_io/read_bed.h -include/PacBio/seqan/bed_io/write_bed.h -include/PacBio/seqan/consensus.h -include/PacBio/seqan/consensus/consensus_aligner.h -include/PacBio/seqan/consensus/consensus_aligner_interface.h -include/PacBio/seqan/consensus/consensus_alignment_options.h 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-include/PacBio/seqan/stream/iostream_bzip2.h -include/PacBio/seqan/stream/iostream_bzip2_impl.h -include/PacBio/seqan/stream/iostream_zip.h -include/PacBio/seqan/stream/iostream_zip_impl.h -include/PacBio/seqan/stream/iostream_zutil.h -include/PacBio/seqan/stream/iter_stream.h -include/PacBio/seqan/stream/lexical_cast.h -include/PacBio/seqan/stream/stream_base.h -include/PacBio/seqan/stream/stream_compressor.h -include/PacBio/seqan/stream/tokenization.h -include/PacBio/seqan/stream/virtual_stream.h -include/PacBio/seqan/system.h -include/PacBio/seqan/system/file_async.h -include/PacBio/seqan/system/file_directory.h -include/PacBio/seqan/system/file_forwards.h -include/PacBio/seqan/system/file_sync.h -include/PacBio/seqan/system/system_base.h -include/PacBio/seqan/system/system_condition.h -include/PacBio/seqan/system/system_critical_section.h -include/PacBio/seqan/system/system_event.h -include/PacBio/seqan/system/system_forwards.h -include/PacBio/seqan/system/system_mutex.h -include/PacBio/seqan/system/system_thread.h -include/PacBio/seqan/translation.h -include/PacBio/seqan/translation/translation.h -include/PacBio/seqan/translation/translation_tables.h -include/PacBio/seqan/ucsc_io.h -include/PacBio/seqan/ucsc_io/ucsc_file.h -include/PacBio/seqan/ucsc_io/ucsc_io.h -include/PacBio/seqan/ucsc_io/ucsc_record.h -include/PacBio/seqan/vcf_io.h -include/PacBio/seqan/vcf_io/read_vcf.h -include/PacBio/seqan/vcf_io/vcf_file.h -include/PacBio/seqan/vcf_io/vcf_header.h -include/PacBio/seqan/vcf_io/vcf_header_record.h -include/PacBio/seqan/vcf_io/vcf_io_context.h -include/PacBio/seqan/vcf_io/vcf_record.h -include/PacBio/seqan/vcf_io/write_vcf.h -include/PacBio/seqan/version.h