FreeBSD Bugzilla – Attachment 174772 Details for
Bug 212682
[MAINTAINER] update biology/seqan and biology/seqan-apps to 2.2.0
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[patch]
bring biology/seqan to 2.2.0
update_biology_seqan.patch (text/plain), 10.86 KB, created by
Hannes Hauswedell
on 2016-09-14 10:32:01 UTC
(
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Description:
bring biology/seqan to 2.2.0
Filename:
MIME Type:
Creator:
Hannes Hauswedell
Created:
2016-09-14 10:32:01 UTC
Size:
10.86 KB
patch
obsolete
>diff -ru seqanOLD/Makefile seqan/Makefile >--- seqanOLD/Makefile 2016-05-27 18:10:36.000000000 +0200 >+++ seqan/Makefile 2016-09-14 11:53:05.324988229 +0200 >@@ -2,8 +2,7 @@ > # $FreeBSD: head/biology/seqan/Makefile 415945 2016-05-27 16:10:36Z amdmi3 $ > > 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} >diff -ru seqanOLD/distinfo seqan/distinfo >--- seqanOLD/distinfo 2016-05-10 03:05:23.000000000 +0200 >+++ seqan/distinfo 2016-09-14 11:53:10.581672651 +0200 >@@ -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 >diff -ru seqanOLD/pkg-plist seqan/pkg-plist >--- seqanOLD/pkg-plist 2016-05-27 18:10:36.000000000 +0200 >+++ seqan/pkg-plist 2016-09-14 12:14:23.714392257 +0200 >@@ -2,12 +2,14 @@ > 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_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_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_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/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_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_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_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/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_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_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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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 @@ > %%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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Flags:
h2+fbsdports
:
maintainer-approval+
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bug 212682
: 174772 |
174773