diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/seqan3/Makefile | 17 | ||||
| -rw-r--r-- | biology/seqan3/distinfo | 12 | ||||
| -rw-r--r-- | biology/seqan3/files/patch-cmake_CPM.cmake | 11 | ||||
| -rw-r--r-- | biology/seqan3/pkg-plist | 132 |
4 files changed, 40 insertions, 132 deletions
diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile index 9c8fc69ba93e..c1675008fd19 100644 --- a/biology/seqan3/Makefile +++ b/biology/seqan3/Makefile @@ -1,10 +1,16 @@ PORTNAME= seqan3 -DISTVERSION= 3.3.0 +DISTVERSION= 3.4.0 CATEGORIES= biology devel math +MASTER_SITES= https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.0/:cpm +DISTFILES= CPM.cmake:cpm +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} \ + xxsds-sdsl-lite-d54d389_GH0${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= C++ header-only library for biological sequence analysis -WWW= https://github.com/seqan/seqan3 +WWW= https://www.seqan.de/ \ + https://github.com/seqan/seqan3 LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md @@ -15,14 +21,13 @@ BUILD_DEPENDS= ${HPP_DEPENDS} RUN_DEPENDS= ${HPP_DEPENDS} \ coin-or-lemon>0:math/lemon -USES= cmake localbase +USES= cmake compiler:c++23-lang localbase USE_GITHUB= yes GH_ACCOUNT= seqan GH_TUPLE= xxsds:sdsl-lite:d54d389:sdsl_lite/submodules/sdsl-lite -USE_GCC= yes # tests only pass with gcc, see https://github.com/seqan/seqan3/issues/2643, otherwise gcc isn't needed because this is a header-only library -# tests fail to compile, see https://github.com/seqan/seqan3/issues/3191 +CMAKE_ARGS= -DCPM_LOCATION=${DISTDIR}/${DIST_SUBDIR} TEST_WRKSRC= ${WRKSRC}/.test @@ -33,7 +38,7 @@ post-install: do-test: @${MKDIR} ${TEST_WRKSRC} && cd ${TEST_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${WRKSRC}/test/unit && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFETCHCONTENT_FULLY_DISCONNECTED=OFF ${WRKSRC}/test/unit && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ctest diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo index 8fa5387420f9..9e9fe56de4ee 100644 --- a/biology/seqan3/distinfo +++ b/biology/seqan3/distinfo @@ -1,5 +1,7 @@ -TIMESTAMP = 1694368553 -SHA256 (seqan-seqan3-3.3.0_GH0.tar.gz) = 96975406445c8a5974803eefa146ee2f85206f6d2c2bccf45171ee0b1a653fb8 -SIZE (seqan-seqan3-3.3.0_GH0.tar.gz) = 1564852 -SHA256 (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1 -SIZE (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835 +TIMESTAMP = 1756395731 +SHA256 (seqan3-3.4.0/CPM.cmake) = 2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a +SIZE (seqan3-3.4.0/CPM.cmake) = 44969 +SHA256 (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 8e000e6788f1e2ada071b36f64231d56f18e2d687ab4122d86cd3aefc6c87743 +SIZE (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 1749810 +SHA256 (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1 +SIZE (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835 diff --git a/biology/seqan3/files/patch-cmake_CPM.cmake b/biology/seqan3/files/patch-cmake_CPM.cmake new file mode 100644 index 000000000000..c288163d7312 --- /dev/null +++ b/biology/seqan3/files/patch-cmake_CPM.cmake @@ -0,0 +1,11 @@ +--- cmake/CPM.cmake.orig 2025-08-28 15:36:29 UTC ++++ cmake/CPM.cmake +@@ -16,7 +16,7 @@ get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DO + # Expand relative path. This is important if the provided path contains a tilde (~) + get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE) + +-file (DOWNLOAD https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake ++file (DOWNLOAD file://${CPM_LOCATION}/CPM.cmake + ${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM}) + + include (${CPM_DOWNLOAD_LOCATION}) diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist index 19d86e63d82e..e727ba232e45 100644 --- a/biology/seqan3/pkg-plist +++ b/biology/seqan3/pkg-plist @@ -91,6 +91,7 @@ include/seqan3/alignment/scoring/all.hpp include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp +include/seqan3/alignment/scoring/hamming_scoring_scheme.hpp include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp include/seqan3/alignment/scoring/scoring_scheme_base.hpp include/seqan3/alignment/scoring/scoring_scheme_concept.hpp @@ -191,11 +192,16 @@ include/seqan3/contrib/README.md include/seqan3/contrib/parallel/buffer_queue.hpp include/seqan3/contrib/parallel/serialised_resource_pool.hpp include/seqan3/contrib/parallel/suspendable_queue.hpp +include/seqan3/contrib/sdsl-lite.hpp include/seqan3/contrib/std/.clang-format include/seqan3/contrib/std/.gitignore -include/seqan3/contrib/std/LICENSE +include/seqan3/contrib/std/LICENSE.md +include/seqan3/contrib/std/LICENSES/BSD-3-Clause.txt +include/seqan3/contrib/std/LICENSES/CC-BY-4.0.txt +include/seqan3/contrib/std/LICENSES/CC0-1.0.txt include/seqan3/contrib/std/README.md include/seqan3/contrib/std/all_view.hpp +include/seqan3/contrib/std/chunk_by_view.hpp include/seqan3/contrib/std/chunk_view.hpp include/seqan3/contrib/std/concepts.hpp include/seqan3/contrib/std/detail/adaptor_base.hpp @@ -203,7 +209,9 @@ include/seqan3/contrib/std/detail/adaptor_for_view_without_args.hpp include/seqan3/contrib/std/detail/adaptor_from_functor.hpp include/seqan3/contrib/std/detail/compiler_definitions.hpp include/seqan3/contrib/std/detail/exposition_only.hpp +include/seqan3/contrib/std/detail/movable_box.hpp include/seqan3/contrib/std/detail/non_propagating_cache.hpp +include/seqan3/contrib/std/enumerate_view.hpp include/seqan3/contrib/std/join_with_view.hpp include/seqan3/contrib/std/pair.hpp include/seqan3/contrib/std/to.hpp @@ -239,14 +247,13 @@ include/seqan3/core/debug_stream.hpp include/seqan3/core/debug_stream/all.hpp include/seqan3/core/debug_stream/byte.hpp include/seqan3/core/debug_stream/debug_stream_type.hpp +include/seqan3/core/debug_stream/default_printer.hpp include/seqan3/core/debug_stream/detail/to_string.hpp include/seqan3/core/debug_stream/optional.hpp include/seqan3/core/debug_stream/range.hpp include/seqan3/core/debug_stream/tuple.hpp include/seqan3/core/debug_stream/variant.hpp include/seqan3/core/detail/all.hpp -include/seqan3/core/detail/all_view.hpp -include/seqan3/core/detail/copyable_wrapper.hpp include/seqan3/core/detail/customisation_point.hpp include/seqan3/core/detail/deferred_crtp_base.hpp include/seqan3/core/detail/empty_type.hpp @@ -364,127 +371,10 @@ include/seqan3/search/views/minimiser.hpp include/seqan3/search/views/minimiser_hash.hpp include/seqan3/std/charconv include/seqan3/std/new -include/seqan3/submodules/sdsl-lite/include/sdsl/.gitignore -include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bits.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_g.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_gg.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_comma.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_delta.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_gamma.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_fibonacci.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/config.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_bwt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_config.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_isa.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa_se.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_bitcompressed.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_wt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_fully.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_iterators.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sct3.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/dac_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/divsufsort.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/enc_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/fast_cache.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/hyb_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_buffer.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_mapper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/inv_perm_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/io.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/iterators.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_byte.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_dac.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree2.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_vlc.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_wt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/louds_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/memory_management.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/memory_tracking.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/platform.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/qsufsort.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/ram_filebuf.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/ram_fs.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_v.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v5.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector_15.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sd_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sdsl_concepts.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_mcl.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sfstream.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_int_stack.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_stack_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/structure_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_arrays.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_trees.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uint128_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uint256_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uintx_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/util.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/vectors.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/vlc_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wavelet_trees.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wm_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_ap.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_blcd.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_epr.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_gmr.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_huff.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_hutu.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_pc.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_rlmn.hpp include/seqan3/utility/all.hpp include/seqan3/utility/bloom_filter/all.hpp include/seqan3/utility/bloom_filter/bloom_filter.hpp +include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp include/seqan3/utility/char_operations/all.hpp include/seqan3/utility/char_operations/predicate.hpp include/seqan3/utility/char_operations/predicate_detail.hpp |