Date: Wed, 14 Sep 2016 19:38:58 +0000 (UTC) From: Pawel Pekala <pawel@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r422156 - in head/biology: seqan seqan-apps Message-ID: <201609141938.u8EJcwkC081135@repo.freebsd.org>
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Author: pawel Date: Wed Sep 14 19:38:58 2016 New Revision: 422156 URL: https://svnweb.freebsd.org/changeset/ports/422156 Log: - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1] - Fix spelling in pkg-descr PR: 212682 [1] Submitted by: Hannes Hauswedell (maintainer) [1] Modified: head/biology/seqan-apps/Makefile head/biology/seqan-apps/distinfo head/biology/seqan-apps/pkg-descr head/biology/seqan/Makefile head/biology/seqan/distinfo head/biology/seqan/pkg-plist Modified: head/biology/seqan-apps/Makefile ============================================================================== --- head/biology/seqan-apps/Makefile Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan-apps/Makefile Wed Sep 14 19:38:58 2016 (r422156) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= seqan-apps -PORTVERSION= 2.1.1 +PORTVERSION= 2.2.0 DISTVERSIONPREFIX= seqan-v CATEGORIES= biology Modified: head/biology/seqan-apps/distinfo ============================================================================== --- head/biology/seqan-apps/distinfo Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan-apps/distinfo Wed Sep 14 19:38:58 2016 (r422156) @@ -1,2 +1,3 @@ -SHA256 (seqan-seqan-seqan-v2.1.1_GH0.tar.gz) = df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c -SIZE (seqan-seqan-seqan-v2.1.1_GH0.tar.gz) = 110874831 +TIMESTAMP = 1473848209 +SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8 +SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119 Modified: head/biology/seqan-apps/pkg-descr ============================================================================== --- head/biology/seqan-apps/pkg-descr Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan-apps/pkg-descr Wed Sep 14 19:38:58 2016 (r422156) @@ -5,7 +5,7 @@ focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some -applications are packaged seperately and the library +applications are packaged separately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ Modified: head/biology/seqan/Makefile ============================================================================== --- head/biology/seqan/Makefile Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan/Makefile Wed Sep 14 19:38:58 2016 (r422156) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= seqan -PORTVERSION= 2.1.1 -PORTREVISION= 1 +PORTVERSION= 2.2.0 CATEGORIES= biology MASTER_SITES= http://packages.seqan.de/seqan-library/ DISTNAME= ${PORTNAME}-library-${PORTVERSION} Modified: head/biology/seqan/distinfo ============================================================================== --- head/biology/seqan/distinfo Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan/distinfo Wed Sep 14 19:38:58 2016 (r422156) @@ -1,2 +1,3 @@ -SHA256 (seqan-library-2.1.1.tar.xz) = 8926f91fec5ce57e8efc70ac16cbf041bde0e0be463685b86e0d2e1e6a8169d7 -SIZE (seqan-library-2.1.1.tar.xz) = 5238884 +TIMESTAMP = 1473846790 +SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd +SIZE (seqan-library-2.2.0.tar.xz) = 5223004 Modified: head/biology/seqan/pkg-plist ============================================================================== --- head/biology/seqan/pkg-plist Wed Sep 14 19:27:59 2016 (r422155) +++ head/biology/seqan/pkg-plist Wed Sep 14 19:38:58 2016 (r422156) @@ -2,12 +2,14 @@ include/seqan/align.h include/seqan/align/align_base.h include/seqan/align/align_cols.h include/seqan/align/align_config.h +include/seqan/align/align_interface_wrapper.h include/seqan/align/align_iterator_base.h include/seqan/align/align_metafunctions.h include/seqan/align/align_traceback.h include/seqan/align/alignment_algorithm_tags.h include/seqan/align/alignment_operations.h include/seqan/align/dp_algorithm_impl.h +include/seqan/align/dp_align_simd_helper.h include/seqan/align/dp_band.h include/seqan/align/dp_cell.h include/seqan/align/dp_cell_affine.h @@ -27,6 +29,7 @@ include/seqan/align/dp_matrix_sparse.h include/seqan/align/dp_meta_info.h include/seqan/align/dp_profile.h include/seqan/align/dp_scout.h +include/seqan/align/dp_scout_simd.h include/seqan/align/dp_setup.h include/seqan/align/dp_trace_segment.h include/seqan/align/dp_traceback_adaptor.h @@ -336,6 +339,10 @@ include/seqan/index/find_pigeonhole.h include/seqan/index/find_quasar.h include/seqan/index/find_swift.h include/seqan/index/index_base.h +include/seqan/index/index_bidirectional.h +include/seqan/index/index_bidirectional_stree.h +include/seqan/index/index_bifm.h +include/seqan/index/index_bifm_stree.h include/seqan/index/index_bwt.h include/seqan/index/index_childtab.h include/seqan/index/index_device.h @@ -348,7 +355,6 @@ include/seqan/index/index_esa_stree.h include/seqan/index/index_fm.h include/seqan/index/index_fm_compressed_sa.h include/seqan/index/index_fm_compressed_sa_iterator.h -include/seqan/index/index_fm_device.h include/seqan/index/index_fm_dox.h include/seqan/index/index_fm_lf_table.h include/seqan/index/index_fm_rank_dictionary_base.h @@ -444,7 +450,6 @@ include/seqan/misc/accumulators.h include/seqan/misc/base.h include/seqan/misc/bit_twiddling.h include/seqan/misc/bit_twiddling_functors.h -include/seqan/misc/cuda.h include/seqan/misc/dequeue.h include/seqan/misc/edit_environment.h include/seqan/misc/interval_tree.h @@ -464,6 +469,7 @@ include/seqan/modifier/modifier_alphabet include/seqan/modifier/modifier_cyclic_shape.h include/seqan/modifier/modifier_functors.h include/seqan/modifier/modifier_iterator.h +include/seqan/modifier/modifier_padding.h include/seqan/modifier/modifier_position.h include/seqan/modifier/modifier_reverse.h include/seqan/modifier/modifier_shortcuts.h @@ -505,10 +511,6 @@ include/seqan/pipe/pool_base.h include/seqan/pipe/pool_mapper.h include/seqan/pipe/pool_sorter.h include/seqan/platform.h -include/seqan/platform/platform_gcc.h -include/seqan/platform/platform_icc.h -include/seqan/platform/platform_nvcc.h -include/seqan/platform/platform_windows.h include/seqan/random.h include/seqan/random/random_base.h include/seqan/random/random_beta.h @@ -536,7 +538,9 @@ include/seqan/score/score_base.h include/seqan/score/score_edit.h include/seqan/score/score_matrix.h include/seqan/score/score_matrix_data.h +include/seqan/score/score_matrix_dyn.h include/seqan/score/score_matrix_io.h +include/seqan/score/score_simd_wrapper.h include/seqan/score/score_simple.h include/seqan/seeds.h include/seqan/seeds/banded_chain_alignment.h @@ -569,7 +573,6 @@ include/seqan/seq_io/sequence_file.h include/seqan/sequence.h include/seqan/sequence/adapt_array_pointer.h include/seqan/sequence/adapt_stl_container.h -include/seqan/sequence/adapt_thrust_vector.h include/seqan/sequence/container_view.h include/seqan/sequence/container_view_zip.h include/seqan/sequence/iter_concat_virtual.h @@ -594,7 +597,6 @@ include/seqan/sequence/string_set_base.h include/seqan/sequence/string_set_concat_direct.h include/seqan/sequence/string_set_dependent_generous.h include/seqan/sequence/string_set_dependent_tight.h -include/seqan/sequence/string_set_device.h include/seqan/sequence/string_set_owner.h include/seqan/sequence/string_set_segment.h include/seqan/sequence/string_set_view.h @@ -649,12 +651,8 @@ include/seqan/system/file_directory.h include/seqan/system/file_forwards.h include/seqan/system/file_sync.h include/seqan/system/system_base.h -include/seqan/system/system_condition.h -include/seqan/system/system_critical_section.h -include/seqan/system/system_event.h +include/seqan/system/system_event_win.h include/seqan/system/system_forwards.h -include/seqan/system/system_mutex.h -include/seqan/system/system_thread.h include/seqan/tabix_io.h include/seqan/tabix_io/tabix_index_tbi.h include/seqan/translation.h @@ -705,6 +703,7 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/class_BedRecord.html %%PORTDOCS%%%%DOCSDIR%%/html/class_BedRgb.html %%PORTDOCS%%%%DOCSDIR%%/html/class_BetaDistribution.html +%%PORTDOCS%%%%DOCSDIR%%/html/class_BidirectionalIndex.html %%PORTDOCS%%%%DOCSDIR%%/html/class_BlastIOContext.html %%PORTDOCS%%%%DOCSDIR%%/html/class_BlastMatch.html %%PORTDOCS%%%%DOCSDIR%%/html/class_BlastMatchField.html @@ -805,6 +804,7 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/class_RankSupportBitString.html %%PORTDOCS%%%%DOCSDIR%%/html/class_ReadStoreElement.html %%PORTDOCS%%%%DOCSDIR%%/html/class_Repeat.html +%%PORTDOCS%%%%DOCSDIR%%/html/class_RevTextFibre.html %%PORTDOCS%%%%DOCSDIR%%/html/class_RightArrayBinaryTree.html %%PORTDOCS%%%%DOCSDIR%%/html/class_RuntimeError.html %%PORTDOCS%%%%DOCSDIR%%/html/class_Score.html @@ -1042,6 +1042,7 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/stream/lexical_cast.cpp.stdout %%PORTDOCS%%%%DOCSDIR%%/html/demos/tutorial/sam_and_bam_io/example.sam %%PORTDOCS%%%%DOCSDIR%%/html/demos/tutorial/sam_and_bam_io/solution1.cpp +%%PORTDOCS%%%%DOCSDIR%%/html/enum_AminoAcidScoreMatrixID.html %%PORTDOCS%%%%DOCSDIR%%/html/enum_ArgParseArgument_58_58ArgumentType.html %%PORTDOCS%%%%DOCSDIR%%/html/enum_ArgumentParser_58_58ParseResult.html %%PORTDOCS%%%%DOCSDIR%%/html/enum_BamFlags.html @@ -1291,6 +1292,7 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringComplement.html %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverse.html %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverseComplement.html +%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_SelectableAminoAcidMatrix.html %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_SimpleScoreTypedef.html %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_TraceBack.html %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_UnicodeString.html @@ -1390,8 +1392,10 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/js/lang_entities.js %%PORTDOCS%%%%DOCSDIR%%/html/js/less.min.js %%PORTDOCS%%%%DOCSDIR%%/html/js/link.data.js +%%PORTDOCS%%%%DOCSDIR%%/html/js/module_tree.js %%PORTDOCS%%%%DOCSDIR%%/html/js/rubydoc_custom.js %%PORTDOCS%%%%DOCSDIR%%/html/js/search.data.js +%%PORTDOCS%%%%DOCSDIR%%/html/js/search.data.module.js %%PORTDOCS%%%%DOCSDIR%%/html/js/search.engine.js %%PORTDOCS%%%%DOCSDIR%%/html/js/version.js %%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/3L.less @@ -1424,6 +1428,8 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/knockout-examples.html %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/less/bootstrap-multiselect.less %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/tests.html +%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-treeview/css/bootstrap-treeview.css +%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-treeview/js/bootstrap-treeview.js %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.css %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.min.css %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.eot @@ -1652,20 +1658,23 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/unit.js %%PORTDOCS%%%%DOCSDIR%%/html/lib/styles.less %%PORTDOCS%%%%DOCSDIR%%/html/list.html -%%PORTDOCS%%%%DOCSDIR%%/html/macro_PLATFORM_95CUDA.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_COMPILER_95CLANG.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_COMPILER_95GCC.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_COMPILER_95LINTEL.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_COMPILER_95MSVC.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_COMPILER_95WINTEL.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_PLATFORM_95GCC.html -%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95DEVICE.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95ENABLE_95PARALLELISM.html -%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95GLOBAL.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HAS_95BZIP2.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HAS_95ZLIB.html -%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HOST.html -%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HOST_95DEVICE.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95IS_9532_95BIT.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95IS_9564_95BIT.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95OMP_95PRAGMA.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95PATH_95TO_95ROOT.html %%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95TEMP_95FILENAME.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_STDLIB_95GNU.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_STDLIB_95LLVM.html +%%PORTDOCS%%%%DOCSDIR%%/html/macro_STDLIB_95VS.html %%PORTDOCS%%%%DOCSDIR%%/html/page_DemoConstraintIterator.html %%PORTDOCS%%%%DOCSDIR%%/html/page_DemoIndexCountChildren.html %%PORTDOCS%%%%DOCSDIR%%/html/page_DemoMaximalRepeats.html @@ -1784,6 +1793,8 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/specialization_MaxRepeatsIterator.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModCyclicShapeModifiedIterator.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModCyclicShapeModifiedString.html +%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModPaddingIterator.html +%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModPaddingString.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModReverseIterator.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModReverseString.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModViewModifiedIterator.html @@ -1829,6 +1840,7 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileIn.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileOut.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Sampler.html +%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ScoreSimdWrapper.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileIn.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileOut.html %%PORTDOCS%%%%DOCSDIR%%/html/specialization_SetHorspoolPattern.html @@ -1899,5 +1911,3 @@ share/cmake/Modules/FindSeqAn.cmake %%PORTDOCS%%%%DOCSDIR%%/html/tag_Nothing.html %%PORTDOCS%%%%DOCSDIR%%/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html %%PORTDOCS%%%%DOCSDIR%%/html/variable_LibraryStoreElementstd.html -%%PORTDOCS%%@dir %%DOCSDIR%%/html/docs/seqan -%%PORTDOCS%%@dir %%DOCSDIR%%/html/lists
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