R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

easyblock = 'Bundle'

name = 'R-bundle-Bioconductor'
version = '3.16'
versionsuffix = '-R-%(rver)s'

homepage = 'https://bioconductor.org'
description = """Bioconductor provides tools for the analysis and coprehension
 of high-throughput genomic data."""

toolchain = {'name': 'foss', 'version': '2022b'}

builddependencies = [('pkgconf', '1.9.3')]

dependencies = [
    ('R', '4.2.2'),
    ('Boost', '1.81.0'),  # for mzR
    ('GSL', '2.7'),  # for flowClust
    ('HDF5', '1.14.0'),  # for rhdf5
    ('arrow-R', '11.0.0.3', versionsuffix),  # required by RcisTarget
]

exts_default_options = {
    'source_urls': [
        'https://bioconductor.org/packages/3.16/bioc/src/contrib/',
        'https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/%(name)s',
        'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/',
        'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/',
        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
        'https://cran.r-project.org/src/contrib/',  # current version of packages
        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
    ],
    'source_tmpl': '%(name)s_%(version)s.tar.gz'
}

exts_defaultclass = 'RPackage'

# check whether correct version is installed in extension filter
# (some versions in this bundle may be newer than the ones provided by R)
local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') "
local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))

# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
# !! order of packages is important !!
# packages updated on 18th March 2023
exts_list = [
    ('BiocGenerics', '0.44.0', {
        'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'],
    }),
    ('Biobase', '2.58.0', {
        'checksums': ['db798af54eb18d83242b1ffbb1fa35b5bc0256cedf86b9a6519e2d786d20e566'],
    }),
    ('S4Vectors', '0.36.2', {
        'checksums': ['68b441289882bde641a1d736287b2dfb837c21b21e18b127b9fee1fc5d792c8c'],
    }),
    ('IRanges', '2.32.0', {
        'checksums': ['097935916b5cb33804e1ea09fa6c4ee7ddeaa03eef99138a05b1896b28dc6a4b'],
    }),
    ('GenomeInfoDbData', '1.2.9', {
        'checksums': ['e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa'],
    }),
    ('GenomeInfoDb', '1.34.9', {
        'checksums': ['2bbb094636bf628447ed4c49b4cd96c164264d012a59f0fe5982f12e6a6bc956'],
    }),
    ('zlibbioc', '1.44.0', {
        'checksums': ['8b2616b722e2d610cdd41aba1a94b987ab017e0bfff63f6ce66f191e81abe530'],
    }),
    ('XVector', '0.38.0', {
        'checksums': ['e9ba0ec3f4124c6f0ce13c4d562e7e4419f8aa5db4283092574a63a207f4ed79'],
    }),
    ('Biostrings', '2.66.0', {
        'checksums': ['7312c508bc2fe6ea3da75edd621b41a35929f9dbdca16d25eb3724ca2cd206fd'],
    }),
    ('KEGGREST', '1.38.0', {
        'checksums': ['ec9fe4b9e11858ba1236c22c9058ea3b3e6967168c847b01003b15d1afb94318'],
    }),
    ('AnnotationDbi', '1.60.2', {
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    }),
    ('GenomicRanges', '1.50.2', {
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    }),
    ('BiocParallel', '1.32.5', {
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    }),
    ('Rhtslib', '2.0.0', {
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    ('Rsamtools', '2.14.0', {
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    ('DelayedArray', '0.24.0', {
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    ('SummarizedExperiment', '1.28.0', {
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    ('GenomicAlignments', '1.34.1', {
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    }),
    ('ShortRead', '1.56.1', {
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    }),
    ('graph', '1.76.0', {
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    }),
    ('affyio', '1.68.0', {
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    ('preprocessCore', '1.60.2', {
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    }),
    ('BiocManager', '1.30.20', {
        'checksums': ['b9e72d7687abbd785a69fecb530ec86ad92257a6be95b8e15953b193a516d5ea'],
    }),
    ('affy', '1.76.0', {
        'checksums': ['f28162f390369957f4bed64c535c64c1901be151c4642cf456065e45704d3dc6'],
    }),
    ('GO.db', '3.16.0', {
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    }),
    ('limma', '3.54.2', {
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    }),
    ('RBGL', '1.74.0', {
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    }),
    ('org.Hs.eg.db', '3.16.0', {
        'checksums': ['2d2e6fdefa0dbb61c86d4736e5a0d430745ae733e310f240b97b2cb3703a2c0a'],
    }),
    ('AnnotationForge', '1.40.1', {
        'checksums': ['de073ce37a6c661696d4de2e577882c7379af49f20181b6be62896660a658d9b'],
    }),
    ('annaffy', '1.70.0', {
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    }),
    ('gcrma', '2.70.0', {
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    ('oligoClasses', '1.60.0', {
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    ('edgeR', '3.40.2', {
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    ('PFAM.db', '3.16.0', {
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    ('perm', '1.0-0.2', {
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    ('baySeq', '2.31.0', {
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    ('samr', '3.0', {
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    ('DEGseq', '1.52.0', {
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    ('hgu133plus2.db', '3.13.0', {
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    ('illuminaio', '0.40.0', {
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    ('BiocIO', '1.8.0', {
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    ('restfulr', '0.0.15', {
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    ('biomaRt', '2.54.0', {
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        'checksums': ['a968daf40745cc54b48bfe6c2a105d631f88deaeb09008f12d239f6858dd63e3'],
    }),
    ('HiCcompare', '1.20.0', {
        'checksums': ['ae4adc96ef85b0675d2089207ad756dd14152e9127db66cf5b034c07ee1a7b43'],
    }),
    ('ROntoTools', '2.26.0', {
        'checksums': ['1a60b08689b2878761188298cf1969e096741f560e96608612b6ed9145671174'],
    }),
    ('scDblFinder', '1.12.0', {
        'checksums': ['f1eb33ad022e4d1c007f9dae72efb05a3c183cd6eb576794b9a0339f9180543f'],
    }),
    ('treeio', '1.22.0', {
        'checksums': ['892283d09694dd4cc7111118647612d1f2fcd2b730bab1c7a5301de54f2288f6'],
    }),
    ('ggtree', '3.6.2', {
        'checksums': ['bdca865db5cfc5b4aa89f62e185b31d3f1de87658609a7bfe9e0769895c1f69c'],
    }),
    ('scistreer', '1.1.0', {
        'checksums': ['49936bcbb107423d96aee421334c4ac6a1048434d2621b84eab95cf7ac11b731'],
    }),
    ('numbat', '1.2.2', {
        'checksums': ['0c567b26f7ff9a6c2129f9c023ffe6eaccea441b73b91cc3f327d630513c181b'],
    }),
    ('HiCBricks', '1.16.0', {
        'checksums': ['d41a7600003b62ff04e3e3ddbc62e494c325207b3da720e5acefcc03ad06a80e'],
    }),
    ('dir.expiry', '1.6.0', {
        'checksums': ['c8157d9ea86ad244923b344fe39bd73931fe2399e46ba0ae08af8de8980ca3c7'],
    }),
    ('basilisk.utils', '1.10.0', {
        'checksums': ['dca17bf5ca9ae225258241744a9829c71fb07b5450f37cb9a20fbcac104f023e'],
    }),
    ('basilisk', '1.10.2', {
        'checksums': ['09b402dae2d9328f76d7ffb91311cde639e55c967462ed279345caa3e2a84f93'],
    }),
    ('zellkonverter', '1.8.0', {
        'checksums': ['bed7c72324df7882816e594ccd8d6b84f5575999491c89a4ab5739e8a9d9242c'],
    }),
    ('DO.db', '2.9', {
        'checksums': ['762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881'],
    }),
    ('GOSemSim', '2.24.0', {
        'checksums': ['5a78ea253c1c34ef0b2c479eaef295eb766c81658688021ab553df301f3e8c93'],
    }),
    ('HDO.db', '0.99.1', {
        'checksums': ['c17cf28d06621d91148a64d47fdeaa906d8621aba7a688715fb9571a55f7cf92'],
    }),
    ('DOSE', '3.24.2', {
        'checksums': ['6fec12b1d5f622f5606236d559c801072d185c6f64aaf60e749cc7b09e369769'],
    }),
    ('enrichplot', '1.18.3', {
        'checksums': ['f483d3a8e7210a772acec74b4728a3f14812be11ae67072c80e3a35287c8ec5b'],
    }),
    ('gson', '0.1.0', {
        'checksums': ['14ddbee5be66d0b1dc178e41175a50ab6ed9ffed04d4361ecf5eef3548d9a381'],
    }),
    ('clusterProfiler', '4.6.2', {
        'checksums': ['af014c40f46646db0a5b6ef883af6e04010b5c1c0c33b8ff5d30336e43c3fc04'],
    }),
    ('reactome.db', '1.82.0', {
        'checksums': ['82f013e2bf42580c039af74a7fddba17e445cdb4845f95ccd61cfd07bc3cd350'],
    }),
    ('graphite', '1.44.0', {
        'checksums': ['1ccca351d2f6e6c90e76b6a899b08b83a95241a67c1546f50e4f312bc252723e'],
    }),
    ('ReactomePA', '1.42.0', {
        'checksums': ['c2c55cf86b81841303952d9c4d4acac1ad964d31c1f8a5d17ff4679b26242919'],
    }),
    ('flowClean', '1.36.0', {
        'checksums': ['732848b879f4d7bb5b9b4cbef32a6980e93b28fd92913b08456736c01dc21cf3'],
    }),
    ('flowAI', '1.28.0', {
        'checksums': ['e9995350f3076a42f8e9fc65c8cafded12924947da17c361a72f26c4a5a5f9a3'],
    }),
    ('flowFP', '1.56.3', {
        'checksums': ['fe64504cdb419adbb4342686ef0c99906c0071cc626ac12bba9d3161ed3ec611'],
    }),
    ('simplifyEnrichment', '1.8.0', {
        'checksums': ['fe492daf93f39c34b47340182e008ac7140eeb14d02a4e9961f47d693c2c1d8c'],
    }),
    ('RPMG', '2.2-3', {
        'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'],
    }),
    ('Rwave', '2.6-5', {
        'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'],
    }),
    ('RSEIS', '4.1-4', {
        'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'],
    }),
    ('splancs', '2.01-43', {
        'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'],
    }),
    ('MBA', '0.1-0', {
        'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'],
    }),
    ('GEOmap', '2.5-0', {
        'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'],
    }),
    ('RFOC', '3.4-6', {
        'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'],
    }),
    ('flowDensity', '1.32.0', {
        'checksums': ['4977c5a2723a034a9fb9458bfba00f917fa87182af35198f82d24d75f4c1d4bd'],
    }),
    ('flowPeaks', '1.44.0', {
        'checksums': ['97ad0e513cfb954eef35445ee085d1d6268d0ab2a8ec4e73d6456ea6d25a7a58'],
    }),
    ('SamSPECTRAL', '1.52.0', {
        'checksums': ['b8f85ce42b62b42c6fe6fd7fac7501e4329a359ad9126190207da9607c88f0ea'],
    }),
    ('ddPCRclust', '1.18.0', {
        'checksums': ['c27706a922d11d49a0a4f269df9de6882d81140eecf8a726220cd52b6db8372c'],
    }),
    ('feature', '1.2.15', {
        'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'],
    }),
    ('flowMerge', '2.46.0', {
        'checksums': ['3634723fd87b1bae71e2cd9e646e98cecc891521b4f2e9ff3ff388362b8b21eb'],
    }),
    ('SpatialExperiment', '1.8.1', {
        'checksums': ['0fdfc5642dde227b73d81812b6641f2d10223de66892b9d61ac80664cd6cbacd'],
    }),
    ('TrajectoryUtils', '1.6.0', {
        'checksums': ['03f0ef8643c0a8be48e042efe5b17ce1840719dd70f16151216fe6aaef261c8c'],
    }),
    ('slingshot', '2.6.0', {
        'checksums': ['6348ecd10a1572593de1d329318f03d8b1352dc041290a092d25a72f5a8c0902'],
    }),
    ('TreeSummarizedExperiment', '2.6.0', {
        'checksums': ['82aa3d7ec6935f5bd8fde3d1be38f9827c6bf2bd2a1af98889a9001aec7ddf8c'],
    }),
    ('decontam', '1.18.0', {
        'checksums': ['02b95f72c76af5abbc5d2febbb2f51b88fab76ebc355b45252bc5bea848a672e'],
    }),
    ('DECIPHER', '2.26.0', {
        'checksums': ['c10e55204abbfb691a697f40a5527d8e1d645710f43459fad553ece24aeb1f06'],
    }),
    ('mia', '1.6.0', {
        'checksums': ['ccfaca9cc948778e10bc6157fa95f69db0157c7abcc7cf1b63b934b3df43e87b'],
    }),
    ('ANCOMBC', '2.0.2', {
        'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'],
    }),
    ('decoupleR', '2.4.0', {
        'checksums': ['b141afd331449b0b1c2dc3dc3097465c2c02b5026129d8f06dd5bfb445bce2a0'],
    }),
    ('UCell', '2.2.0', {
        'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'],
    }),
    ('intervals', '0.15.4', {
        'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'],
    }),
    ('oompaBase', '3.2.9', {
        'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'],
    }),
    ('oompaData', '3.1.3', {
        'checksums': ['aeb932f75d3de2101d2e1b387fe76677f2d38d4819710320c0e3df07df3ab73d'],
    }),
    ('TailRank', '3.2.2', {
        'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'],
    }),
    ('RnBeads', '2.16.0', {
        'checksums': ['459c14a98be9056b844b9c44b865a76f30e38edbfef3592ac79c2c261d6f5fb2'],
    }),
    ('RnBeads.hg19', '1.30.0', {
        'checksums': ['d20a968f7a7d5980f4a0dadfd3b1044245fdefa48985951dffcd6258abaa5e01'],
    }),
    ('RnBeads.hg38', '1.30.0', {
        'checksums': ['b7c9ff2ba2c280a9160d7782571636d8a3868fe2f2882c08839a0a70e7f85e39'],
    }),
    ('RnBeads.mm9', '1.30.0', {
        'checksums': ['ed370096cc8590a41ebdb81153be5499bc3c8cf4f79e1ee67744ec06f96d439f'],
    }),
    ('RnBeads.mm10', '2.6.0', {
        'checksums': ['b655d2b0b056047ab88537fd8a3453eb5677feb5a6cda6206b3350d9a62ba571'],
    }),
    ('RnBeads.rn5', '1.30.0', {
        'checksums': ['e92ab6c298042f16cf0dbcf72fda8ab23877324598a9750cf98281ed0a453191'],
    }),
    ('log4r', '0.4.3', {
        'checksums': ['dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c'],
    }),
    ('MSstatsConvert', '1.8.3', {
        'checksums': ['3deafb978100695037f97bcb458cfd5c76034440435d104a096459190ddd0891'],
    }),
    ('MSstats', '4.6.5', {
        'checksums': ['9a573976fb0fcb4b9d3e6cce831770305205ff8c46e30af4f4e4ba12ccc9fd89'],
    }),
    ('MSstatsTMT', '2.6.1', {
        'checksums': ['f1bf45345b4c6e14b0977d50016dc5925ee154d63a4765e218d1453d9e6fbbc0'],
    }),
    ('MSstatsPTM', '2.0.3', {
        'checksums': ['fe0106c66311f47f4e391528939b4aa6a690e2049b3638c4f5055fdc7b7210d8'],
    }),
    ('factoextra', '1.0.7', {
        'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'],
    }),
    ('MSstatsLiP', '1.4.1', {
        'checksums': ['ccc5b10a7310c5197a21b88cbd365bbba34d799a948d7e120114dfd047064142'],
    }),
    ('babelgene', '22.9', {
        'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'],
    }),
    ('msigdbr', '7.5.1', {
        'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'],
    }),
    ('escape', '1.8.0', {
        'checksums': ['4d80d2798f07885ae035dbb9d994c707ed3a94fbe6cef5f35da51a50cc4168f1'],
    }),
]

modextrapaths = {'R_LIBS_SITE': ''}

sanity_check_paths = {
    'files': [],
    'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'],
}

moduleclass = 'bio'