diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb new file mode 100644 index 000000000000..8a4f0dec1a28 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.17' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = "ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'] + +dependencies = [ + ('R', '4.1.0'), + ('netCDF', '4.8.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb new file mode 100644 index 000000000000..05c3d062d719 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -0,0 +1,1059 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.13' +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': '2021a'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('R', '4.1.0'), + ('Boost', '1.76.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.10.7'), # for rhdf5 + ('ncdf4', '1.17', versionsuffix), # for mzR +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.13/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.13/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 3rd June 2021 +exts_list = [ + ('BiocGenerics', '0.38.0', { + 'checksums': ['a692fe68256578fc1beb60630cfd45ffc3b003ad36801dce8970c4e9eba767cf'], + }), + ('Biobase', '2.52.0', { + 'checksums': ['79abe91af6c5c133582fd08d2035f65034ad90eae5b81b74fa147e6010e2e8e9'], + }), + ('S4Vectors', '0.30.0', { + 'checksums': ['98dce0f9a5f92419e6fa5ce4237e1b352c964b2ad4fd5afddbf108055eedbb6c'], + }), + ('IRanges', '2.26.0', { + 'checksums': ['7d1e8fcbd1f9fc9005765e216418d819775452a77e48a59b80347eb93047f237'], + }), + ('GenomeInfoDbData', '1.2.6', { + 'checksums': ['09209adea5f0ea69535b27710b191f2679f83ccc0bd4342a4d91a9dcf0f91f31'], + }), + ('GenomeInfoDb', '1.28.0', { + 'checksums': ['c36427b5689db58cb1489e6e6c0fd5ce1244ad6fb2d4bf1a7334e579a03e4d72'], + }), + ('zlibbioc', 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['05ab1ef36e9f5d3b4583929d5c461bc863aed9674fea0267edf58ebe5681302b'], + }), + ('MatrixGenerics', '1.4.0', { + 'checksums': ['ba88596471c750d3ec07f0f4ab359dc60dfcbb5e2d8f60a175bc88a0695203f7'], + }), + ('DelayedArray', '0.18.0', { + 'checksums': ['59e2f53c97ccac0f74015bbb50ba576da4afec615b1a9df0b6ece3268c10c370'], + }), + ('SummarizedExperiment', '1.22.0', { + 'checksums': ['2f58077942686218a01ef5645a41516a71eea7f666450a2b32713d69662cd79a'], + }), + ('GenomicAlignments', '1.28.0', { + 'checksums': ['e242de78aab5ba1d8f1d4f72801b5915cdaef544f017305fb709c12941083803'], + }), + ('ShortRead', '1.50.0', { + 'checksums': ['e372bcda18598826a445fc3116f7b226689e63fc717e680b0bbb40c306b7117f'], + }), + ('graph', '1.70.0', { + 'checksums': ['aa6701bad9af248cd4174e0874472244daa9f01e4d636ccd7c84cfd2500afac4'], + }), + ('affyio', '1.62.0', { + 'checksums': ['595ead901fa87b8b625ef94e727cccf31c042f2286288cb1010f2154355e711e'], + }), + ('preprocessCore', '1.54.0', { + 'installopts': 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'checksums': ['1f6678274dfa387baf27fb462f979ab18bf7d6131ae0d5c9fc791b6a36505134'], + }), + ('goseq', '1.44.0', { + 'checksums': ['1ac4737eafe357060310233258cabdbdfdeb3aea55878c4aca6865d2b5ee191f'], + }), + ('KEGGgraph', '1.52.0', { + 'checksums': ['1ad3699b4b271b9f233f7c11ac8b4a28281e77bc58d6f084fc73e40f0bbcad7f'], + }), + ('GEOquery', '2.60.0', { + 'checksums': ['5581713a5588f18d24e32d27d63d5753f6209c696af66137b2a50dd0d86a134a'], + }), + ('RSpectra', '0.16-0', { + 'checksums': ['aaf1cfc9ffe3a4c6684247899924e1c18306971dfef4bae1dc596a2fb42a64a9'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.16.0', { + 'checksums': ['3ca32e2a7c940828f82aaddd967372357d0fccaecaed780d1b782387732e31c3'], + }), + ('Rhdf5lib', '1.14.0', { + 'checksums': ['07d9c6bc5bc52c38ff6437853518940d37824e71c72b8dc5a21d926f49abf8fa'], + }), + ('rhdf5filters', '1.4.0', { + 'checksums': ['ec2dd94273dfec06f95d52366990fa18e4dc85d2cfb8d548bc9a295188067b8c'], + }), + ('rhdf5', '2.36.0', { + 'checksums': ['7f2adc8e8755fdf7ff0ea55fdf98ae3ed85eb406787440152a22b3e473e2b3a8'], + }), + ('HDF5Array', '1.20.0', { + 'checksums': ['2cef8fc8bba194afa0b84707bb699c29477ae84aa01cb478e78be2f2e985289c'], + }), + ('sparseMatrixStats', '1.4.0', { + 'checksums': ['99d9998a829984c1d9fc2e99abb461749b0d95d052a667a970f6e2e95abb9a46'], + }), + ('DelayedMatrixStats', '1.14.0', { + 'checksums': ['135f3a0618d7f84bb183311eb68430251ab1fdadaaf0eb46199514567f46260b'], + }), + ('minfi', '1.38.0', { + 'checksums': ['b24a9485c3c76875b3463fc585bc874a402f9d7e5cdd7ba7e0cbfcbceffd34a1'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.38.0', { + 'checksums': ['121f4fea4b220b11d7d1bbd1078d76adc1ec5e0564f20af9435d6b220acb81a4'], + }), + ('lumi', '2.44.0', { + 'checksums': ['02408f60eb6f389956d3810e1083c3452334d0d8a1b8754065dd5af79bec4d62'], + }), + ('widgetTools', '1.70.0', { + 'checksums': ['62b531a17e4333b66c47d9f94bffd77bffeb282ac57cd89f55247ae7df7ddda0'], + }), + ('tkWidgets', '1.70.0', { + 'checksums': ['c9d28b42a8b8ff08320476b5869c738ba9f86ddba7197057d5e978aca75da25e'], + }), + ('Mfuzz', '2.52.0', { + 'checksums': ['cb9301d13f8db26ef3035e2ffa2cc875b4636133610b5a4bbc19dbc287a5525a'], + }), + ('admisc', '0.15', { + 'checksums': ['27b7ce48026ec2b28b85870b07ad2d338488f39eb879e9a4bfadb7c78793d549'], + }), + ('venn', '1.10', { + 'checksums': ['65422a158cdc8581182d3d326e448e43ecc3764501a5dab1ccac1234b4f961e4'], + }), + ('maSigPro', '1.64.0', { + 'checksums': ['78055e87db33bff8fd507f189d6cf17207ffcc5c4f32bc3e5d55a3deee695ea4'], + }), + ('SPIA', '2.44.0', { + 'checksums': ['09f121cb778c71579fb516fa0a0f4b0fefdc4aeb5d6cb968ef2a15a63572fa6a'], + }), + ('Gviz', '1.36.1', { + 'checksums': ['e5dd779dc1149450a7e17d88ff8dd177f134ee2046ba06717ecd8c77c19192d6'], + }), + ('cummeRbund', '2.34.0', { + 'checksums': ['5d6aae3fc5a3e7f40be40739bc9dfa6b7ad985984699d60f637a355af3ae7bab'], + }), + ('GenomicFiles', '1.28.0', { + 'checksums': ['7e84594e8a76a173153fa1d482ba0200a3b7c83bb7b3ee0ba78a197e2a0990de'], + }), + ('derfinderHelper', '1.26.0', { + 'checksums': ['abfcbc154acb38363d9f70bb8916cbff0b9feaeac6c918f1a157d3d19deeadf0'], + }), + ('derfinder', '1.26.0', { + 'checksums': ['5b1054ce0d5e68e67b8b0bc7c67b79e774eaa1d2e736d7fab3d012ccfea81faf'], + }), + ('polyester', '1.28.0', { + 'checksums': ['c059e37a9ea0c9edadc213ec0874eec84e05adde9fbc0ebb08134841dcb9f038'], + }), + ('Rsubread', '2.6.1', { + 'checksums': ['c8fc4d32e0cf77bf05736edc1f9775eb2e69ad8251c937db07234138fb5ef700'], + }), + ('pcaMethods', '1.84.0', { + 'checksums': ['65556f989400c46ba0d85f24150bfee49f9012742e86269848be1d446cd798b1'], + }), + ('marray', '1.70.0', { + 'checksums': ['a628561c453d1afb50445bd2743af627939383f81f86616180476c7f31ccf572'], + }), + ('CGHbase', '1.52.0', { + 'checksums': ['4421e120d31622297f7f19151352e3b294e772be75b295da4933a0c4379907dd'], + }), + ('Wrench', '1.10.0', { + 'checksums': ['40ef65d4d7edb92cd1e88dfe4c6902e3b9866f6c1d4ba91560d967e515ae5a7b'], + }), + ('lpsymphony', '1.20.0', { + 'checksums': ['f6433dac3e6e7012f0c9dd873004e9bc0f30b15e4323cfe93fdaa35fee58842b'], + }), + ('IHW', '1.20.0', { + 'checksums': ['dc51f14ae444c419b93ad81fc6c7ba4c6d75640b5c9832e7cb767daf901a692c'], + }), + ('metagenomeSeq', '1.34.0', { + 'checksums': ['67a83c151b536b067568f7773964dbfd9d00f31fe2a2b47eb6d663258ce7dd23'], + }), + ('gdsfmt', '1.28.0', { + 'checksums': ['7e5326e82dfd589c2f79c345683f82d08867628b3c5bb0e4c44aedd3766c3885'], + }), + ('SNPRelate', '1.26.0', { + 'checksums': ['6a4d410903b8cefb3dbf3f7ab7e88c5ac226081c89f1df96d54c421704d27a54'], + }), + ('biomformat', '1.20.0', { + 'checksums': ['c96bd41b5afd0a0b9027a7f485a3d136958bf7b90dd47961d4b7aededa84faf1'], + }), + ('phyloseq', '1.36.0', { + 'checksums': ['f112e646382558fda90ecc7b4af770c42bfdb1463c82f5a6a4695bd701d84fa4'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('zCompositions', '1.3.4', { + 'checksums': ['ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.3', { + 'checksums': ['25bc8c4028c021c7135bd86812265d2cf190bc07b3a412c4406f126c22adb0ae'], + }), + ('ALDEx2', '1.24.0', { + 'checksums': ['14181f57035004dbfad33c509109037862c26b951a90b2a6e3ba57677418e29d'], + }), + ('dada2', '1.20.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '85242fcf2c2f273d72a08869128f2e85d388c709531c1523c241ece8bb9d69f1', # dada2_1.20.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.4.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + 'ca58096dd7bcd104044314b50ed304ccb82af1adbd6f7aaf0c3cb04a0b56eb82', # LEA_3.4.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.20.0', { + 'checksums': ['2e0ab41a6e025acbb51e5681b470e10d91cc2c6f84f6a99f52c25dfd41f6e246'], + }), + ('SingleCellExperiment', '1.14.1', { + 'checksums': ['ffe10077c9617c469f5fb02cdf484f04d9ab10e9a7f1d73a714803ad41878daf'], + }), + ('beachmat', '2.8.0', { + 'checksums': ['0629aacb6631f5ed548f8c45da62d2bbf2ad7d011913db54f01a79b214d4e69a'], + }), + ('RcppAnnoy', '0.0.18', { + 'checksums': ['e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.10.0', { + 'checksums': ['fbe400f8214c4d51c953c1e56b00967b03322507090dd47f4f374a8e426c5132'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.0.0', { + 'checksums': ['06a8606f0ed6129d2bf6237c3fc00767e01635acce57c4ca5e1d2b1ef87626c9'], + }), + ('BiocSingular', '1.8.0', { + 'checksums': ['372b86f6cfc7bb087cfdcbcb7310cc80c432c17bdaa2145ad425b2f2077b1dd0'], + }), + ('scuttle', '1.2.0', { + 'checksums': ['e56b29639a1fa1702c4e96c2210f6eb98c56ae5485917654a8e2172b4a7db5ef'], + }), + ('scater', '1.20.0', { + 'checksums': ['450eb0ea7e768571c5047b8d6d1f9454483b664d894453160f247a57415bf766'], + }), + ('sitmo', '2.0.1', { + 'checksums': ['0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('bluster', '1.2.1', { + 'checksums': ['8f1aebbdd967cb85395194ca56650ddf6196a7ed2ddcbb009eb942ca77691f89'], + }), + ('metapod', '1.0.0', { + 'checksums': ['9b426dae5ef4c289ff5eb02cfdce7fe6e5d9112af101f81571d93fd44ce66cc1'], + }), + ('scran', '1.20.1', { + 'checksums': ['c039eae54a46a8c4b8eb035b6a5854b240d7bf6031a6331f42f826feacb99f46'], + }), + ('SC3', '1.20.0', { + 'checksums': ['9c421a02000f3687b1fe146b92a82d01148ba4f6143012d68f264b54bd2f3d32'], + }), + ('ComplexHeatmap', '2.8.0', { + 'checksums': ['2e102de57cbfb17b40276353eea88870c35b37281a99f7ecce4dda207535894a'], + }), + ('GENIE3', '1.14.0', { + 'checksums': ['2bd011e127b845bde1f8ec90521da831915dca7ae8ae6b47759c14f3d96fa4ec'], + }), + ('dupRadar', '1.22.0', { + 'checksums': ['ca4ece6a714bbbbf5daa62cd78cc3cfefd09eec7be946ccab058e4937295bdbf'], + }), + ('DNAcopy', '1.66.0', { + 'checksums': ['8d30c9b6475bcf954327aa97981551756cabd730e7752a5a384230e34840f855'], + }), + ('sva', '3.40.0', { + 'checksums': ['51ce2d1875715e5efeee98ed371ee730489728218d88d00f5cea6ad79667538a'], + }), + ('ballgown', '2.24.0', { + 'checksums': ['211eccb48e3356885dba01c29e2897296ab8cc789439a5081651fde72ef9c839'], + }), + ('DropletUtils', '1.12.1', { + 'checksums': ['298f644106103ad3efd64c34251af81544e38dbd28e0cb8f40e20548fccacf77'], + }), + ('DeconRNASeq', '1.34.0', { + 'checksums': ['e480ec254f26aedc439681faec66ebcf6ad00322786be31c72c2c4dd02093b04'], + }), + ('GSVA', '1.40.0', { + 'checksums': ['0207a189c2fadc3d3d953ce96f673861d5ec06fc8f8ca55e4b5eb334adff4d0d'], + }), + ('PureCN', '1.22.1', { + 'checksums': ['b953c53df361a1ef7ae23d3259628d5edb7b74078174a6b35efff1fa35ba851d'], + }), + ('globaltest', '5.46.0', { + 'checksums': ['3f0ae9b34de6e3daec896ed7583141e056186f45a5fc12957b86251af11429b9'], + }), + ('GlobalAncova', '4.10.0', { + 'checksums': ['320f1a7f36458d67a78eed6f5d7e700f7f34ef90c71cb5e2351df949bb53debc'], + }), + ('vsn', '3.60.0', { + 'checksums': ['5beb0d330a78e30430813344ef934012b34decd068598dcc18e8a33d07bcf75a'], + }), + ('mzID', '1.30.0', { + 'checksums': ['dabf9cca3d3b6bb3a4a8696def386af1be5fd3d898dab0b014c014d5b3335ef3'], + }), + ('mzR', '2.26.0', { + 'patches': ['mzR-2.22.0_use-external-boost.patch'], + 'checksums': [ + '772601b6e053df5a5eef85b98da1b7a5b411b2cfde73496276d9f70cb6ddbdd4', # mzR_2.26.0.tar.gz + '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch + ], + }), + ('MsCoreUtils', '1.4.0', { + 'checksums': ['a8dd139e14777e69851cdf50d8a787d5b6ad90db82b419aad1d2eb6dc451e88d'], + }), + ('MSnbase', '2.18.0', { + 'checksums': ['79d2d4e80984fbbe813c7c1fc576a4df2e4b318bc97938410567bd6fe409fafc'], + }), + ('MassSpecWavelet', '1.58.0', { + 'checksums': ['1f988dbae5037454be066829753aa58b0a38eb757033a07bb278fbf0a21643b3'], + }), + ('xcms', '3.14.0', { + 'checksums': ['9dcff26777cd5a9b9b87450dd8faa5391b2891236b995875985186ff261547bb'], + }), + ('CAMERA', '1.48.0', { + 'checksums': ['bed3d65914791907c604184312eb3d3819d8870ca3f6ca123a7735a9ab3e4688'], + }), + ('fgsea', '1.18.0', { + 'checksums': ['2d3d63bb30a735ae5138fe1fae68a05fbe0dbcc32bcd45ca3efb756b887f0dd6'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.58.0', { + 'checksums': ['7d9008700c0ae754d10d71d68d2819bf3bc83b0aeffb37da78c76c73239c005b'], + }), + ('GWASTools', '1.38.0', { + 'checksums': ['f759070b907b9c320cbfdd61705aea1bc5be5b60d2678c9c9fc1982728cc462b'], + }), + ('SeqArray', '1.32.0', { + 'checksums': ['016f523104bb07ca67fd7aac59bb754b246c531a20ca1d3ff72b9c6770918c5a'], + }), + ('SeqVarTools', '1.30.0', { + 'checksums': ['c7775c0c5db8ca644971d3c0b2bca0ef5705617354b1af160e41158e6e3735ae'], + }), + ('GENESIS', '2.22.0', { + 'checksums': ['a76a60d6d4deb6203fa3e0895f6519c259d08251320a71033dcd31c7edbc62de'], + }), + ('MLInterfaces', '1.72.0', { + 'checksums': ['eb669bf5d39a19d906cc2637537bd32f06203036254d15a56f10bbddf8d9ff46'], + }), + ('pRoloc', '1.32.0', { + 'checksums': ['b758b1d6a8e99de46b71629cbdd8212303b878f4198cb1a8efa4affbdf34dd24'], + }), + ('pRolocdata', '1.30.0', { + 'checksums': ['91482fb61a75ce87ee7a351b1676edac8d539d685d8e3aac465b744055afa8bd'], + }), + ('fresh', '0.2.0', { + 'checksums': ['a92db254ae88e8371efac44efe2cf1f5be7cce62291fdf994ebd68c14dad079d'], + }), + ('waiter', '0.2.1', { + 'checksums': ['85b9efef4d396698ba300e1f20f151ed5dc351e2391653d8eccbdd5bb77ead15'], + }), + ('shinydashboardPlus', '2.0.1', { + 'checksums': ['5b25b510b151a78e25ec679a8abf37ee1d21ca49e437fd0538f5eaa39bce78cd'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.6.0', { + 'checksums': ['764a4876b4466dc10b85b43a91fe01359533b1b5dc1e177ca3d86918fe2e0f90'], + }), + ('pRolocGUI', '2.2.0', { + 'checksums': ['b6309ec2f9a0004e21adc277b164211d93bdc80d2bc31579e437a715d28e8f3f'], + }), + ('EBImage', '4.34.0', { + 'checksums': ['03221ccab083dc65ac2eece74e01e307b5201b141096ff9935a68d545eef6cfc'], + }), + ('GenomicScores', '2.4.0', { + 'checksums': ['dc74b41ca5e3f05c325cafb461112f28b1615dd392f2448e7cf164209d4009ad'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.0', { + 'checksums': ['6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.24.0', { + 'checksums': ['54dbf1302eacd1fee259dad6a20b688b9730d10e2335f0b4ebfe1acac657ff77'], + }), + ('InteractionSet', '1.20.0', { + 'checksums': ['ab1b458afdadbfc1b4b6e96a245901d754f9ceafed5a170e09f6185b658b9d0c'], + }), + ('ChIPpeakAnno', '3.26.0', { + 'checksums': ['f30d7eff4a1653fe96ace7f5e16f155e8cce011ccdd622f3c5e273b272d3d5f2'], + }), + ('seqLogo', '1.58.0', { + 'checksums': ['9755621d3a8725356573c63b40a98e1bdb9ff650bdec089ccb6b190683d4a388'], + }), + ('rGADEM', '2.40.0', { + 'checksums': ['f54b126363bd2b46ba9f56d3626a2efb9a25dac87b0048a69971168b255cb915'], + }), + ('MotifDb', '1.34.0', { + 'checksums': ['7f2c8123ef0cbe7e12ce4670139cf3bdd5e96b14ccf95fd25b98055ecb7b9511'], + }), + ('motifStack', '1.36.0', { + 'checksums': ['f78da2a47c8d8aa045d1be2da456fddd16e849677684547d34641f5e2722c37a'], + }), + ('ATACseqQC', '1.16.0', { + 'checksums': ['b4cfc602a77aa6fc69567af995fdcda3770d9d6f2e5a1fd4952e7f09671f0f99'], + }), + ('ResidualMatrix', '1.2.0', { + 'checksums': ['3becaaa3d668e4a64852b140118e6fc7b212d74c074d76ba554602ae5250fb5c'], + }), + ('batchelor', '1.8.0', { + 'checksums': ['0a474dc558f73c26ad096e6f31a42d956fb916d334151d18ad75d4713901a2f6'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.56.0', { + 'checksums': ['5de0e1baaf497b10fc5f496a881b3349abe6606b4d13dc6a28daf54e02dc51fb'], + }), + ('R.devices', '2.17.0', { + 'checksums': ['c2d4b12949e0faab414c9f7575e39ee9dbf50ea12d858143df529f15ea365fb6'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.22.0', { + 'checksums': ['c50f8be7d7b6bafca440fdd54c957ac0c288904fd69115e996f13274033578fb'], + }), + ('PSCBS', '0.65.0', { + 'checksums': ['3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('Repitools', '1.38.0', { + 'checksums': ['7464394ebd039cd1d57e242ddb71bf02fa35a6d0dc9aafae04c834e021c36a50'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.3', { + 'checksums': ['c29911ca93935e3b9aa6a67e894337dc2ad707405da1500c9898bd0578519ecc'], + }), + ('MEDIPS', '1.44.0', { + 'checksums': ['3128cdc286275faffc792c4a6cf08562cad072be6b9c8595d52353f06151a750'], + }), + ('RProtoBufLib', '2.4.0', { + 'patches': ['RProtoBufLib-2.4.0_fix-protobuf-build.patch'], + 'checksums': [ + 'cb2e6eba5fabea2f3ecc9a97ae25d54f2b5ad14ed08381a83db612af4ed2cdc3', # RProtoBufLib_2.4.0.tar.gz + # RProtoBufLib-2.4.0_fix-protobuf-build.patch + '379e0227b22ee027de3ab22be9667f358de7d176f74aba598e5a3cbf41dc99a3', + ], + }), + ('cytolib', '2.4.0', { + 'checksums': ['db92fc4dc0f0e8546f692b07eb1c1ab12f568705e46b87bf6b6844b039fe8772'], + }), + ('flowCore', '2.4.0', { + 'checksums': ['cc92e084d693928e034bcda4f844eb9545589b5fc6c77637ac3d8f12fb5cb78f'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('mathjaxr', '1.4-0', { + 'checksums': ['ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67'], + }), + ('metap', '1.4', { + 'checksums': ['5fac23d823d0ad4eebc3f97620364e25f7b41f8d0c3579f6c09ec059940b85a5'], + }), + ('uwot', '0.1.10', { + 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], + }), + ('scattermore', '0.7', { + 'checksums': ['f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('SeuratObject', '4.0.2', { + 'checksums': ['64ee97a221ccaa0bbdc1890da9d3e9cf5b3b9fab037095cfb757db5bbb69cb1c'], + }), + ('Seurat', '4.0.3', { + 'checksums': ['75d98696d0cee22eac5154ac26ef94accde5a5b0a140f3bdd60265322d9edfc9'], + }), + ('ALL', '1.34.0', { + 'checksums': ['6c376f3360bbb0aad4b5aad9655cb95d2f9d33a1abd2ba4533bee803988d8b63'], + }), + ('ConsensusClusterPlus', '1.56.0', { + 'checksums': ['0b496182208b41928caeea4cc05f0d66e20bceed8f815aa5d2996f6f41c97698'], + }), + ('flowViz', '1.56.0', { + 'checksums': ['3b30dc5b6ade5880afd3127643314f3b2f86d6ec35ef07e72ff70aee7927a09f'], + }), + ('ncdfFlow', '2.38.0', { + 'checksums': ['c0d9ec37b275e98f717f6ac063a594358a23a4e77bbdca4fb6369bed2c46a8d2'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.4.0', { + 'checksums': ['a933b1526f9090218ed0394e71541bed1cff73b07fadb6c11febf1cd9a5838a9'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '5.1.9', { + 'checksums': ['c8bdf4bd285100c4c7ee89bb67df96dbf1132c1cf2c9ee85c59cad52b696597a'], + }), + ('flowStats', '4.4.0', { + 'checksums': ['a60b93ea5f06f1b225f5e945918f9210b8f789ffa08d0f0e13a55658f1a925fb'], + }), + ('flowClust', '3.30.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", + 'checksums': ['cb9cad23d3dca1c30fba10af661efd63395c49b9bc2b2af55493f799f3adba0f'], + }), + ('openCyto', '2.4.0', { + 'checksums': ['bd20a444c91c4d3e045246a0c5bc33af1f55312fbfc4834b783287794b0b59dd'], + }), + ('ggcyto', '1.20.0', { + 'checksums': ['eff273fae7b6676413dfa2176780b09a3a5b8f5fedb1457abcd67e5209aaa649'], + }), + ('CytoML', '2.4.0', { + 'checksums': ['27e640d0b232df06518c0ac7728d86bfb0e5e4f1d87c1e8ce768de686b3dbe47'], + }), + ('colorRamps', '2.3', { + 'checksums': ['3f10eab0602a42a2e5a79c7c04638be06cbf1e6f23979a1bd95d853e10940b6a'], + }), + ('ggnewscale', '0.4.5', { + 'checksums': ['021c36230ab6a7e90ac47f70ad26c27e2f68e8c109e31d3df2988af694d35ec2'], + }), + ('ggpointdensity', '0.1.0', { + 'checksums': ['3ea646cf183c8bf7869b122a4ee972b53709056ff443ea71551b823524092a31'], + }), + ('FlowSOM', '2.0.0', { + 'checksums': ['02518842b746b40a1d66bc20cd4cfae4b449eea3548ec442f335263edeb907a2'], + }), + ('HMMcopy', '1.34.0', { + 'checksums': ['0277c63e16826ae33a445b1f1e854a354133a451510101d019afb237d26654de'], + }), + ('diffcyt', '1.12.0', { + 'checksums': ['e30f011f466573e965e7a584a05aeba60f46e3179d7865ffc85d5974af886122'], + }), + ('blme', '1.0-5', { + 'checksums': ['679a4f19d34a584c2390ffab37810a31f6834b913fceaa2409d297ccdf912310'], + }), + ('variancePartition', '1.22.0', { + 'checksums': ['f2df15335a81fc55225b05c031dcc98247caf9a4df099d67e5faa277d3131edf'], + }), + ('muscat', '1.6.0', { + 'checksums': ['586c88bd14c23ab0593457a4bf9c89a480ba5d517728251f38ad800e05b6a73e'], + }), + ('IlluminaHumanMethylation450kmanifest', '0.4.0', { + 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], + }), + ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { + 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], + }), + ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.0', { + 'checksums': ['249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15'], + }), + 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['c14f145a982597f32264b37a5f2645206a0bee30dd2584a25cb8e3dc2f9b068f'], + }), + ('sparsesvd', '0.2', { + 'checksums': ['1a1f54d6b0dca6ae83e3f729a1895c91c58bfe55427dacc50ddb0d2c5d32a9f6'], + }), + ('docopt', '0.7.1', { + 'checksums': ['9f473887e4607e9b21fd4ab02e802858d0ac2ca6dad9e357a9d884a47fe4b0ff'], + }), + ('qlcMatrix', '0.9.7', { + 'checksums': ['1ef5e0350cfbdb07fca761fc7251584d39d3da2958ea813498b467e4f7661347'], + }), + ('Signac', '1.2.1', { + 'checksums': ['626e976bef3f4647dbbb7adf2a0d4d650c4b24827f3e09f5f8a9e6fe0dda4bde'], + }), + ('poweRlaw', '0.70.6', { + 'checksums': ['efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191'], + }), + ('CNEr', '1.28.0', { + 'checksums': ['533c7a3053e6b3de8d8e52f7d80cbc06941ec5d2898165cb6d49cc539d7e808f'], + }), + ('DirichletMultinomial', '1.34.0', { + 'checksums': ['546be33fee6b05291ca9fee856538125f259ba7750f91db091df510006907546'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.30.0', { + 'checksums': ['596d30e5ca511035ca0c5a89af83292e6408f680bba50f146548646fc5966fab'], + }), + ('motifmatchr', '1.14.0', { + 'checksums': ['75594c5591aebbdb9d9f15d35c653118e518d2791160dd6ff8926c4a6e1b2eee'], + }), + ('extraDistr', '1.9.1', { + 'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'], + }), + ('PRROC', '1.3.1', { + 'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'], + }), + ('TSP', '1.1-10', { + 'checksums': ['44979f16803806419a94a6b0daeac812f4e7bd52d2fff11561fd4bbc41353b7c'], + }), + ('qap', '0.1-1', { + 'checksums': ['60bd564bb0e6325de44351af33870177d84b1c00ded142a2efb12a16a20d4d34'], + }), + ('seriation', '1.2-9', { + 'checksums': ['8b9279caf60755377ee9023971bff33634f7bb9c055d4ebb493b648512b09dbe'], + }), + ('egg', '0.4.5', { + 'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'], + }), + ('heatmaply', '1.2.1', { + 'checksums': ['2dddf6741eaaa49c1354b7092ded5ac6d06df9d6accd879c16c6731bed745743'], + }), + ('OUTRIDER', '1.10.0', { + 'checksums': ['4180041609e3668232155df1ce3658735d2825ca2116e4e13ce687c112176cef'], + }), + ('FRASER', '1.4.0', { + 'checksums': ['5205d8623ce0e5629a49aa092e4aa3350fc5d1a4575130400b1e61115f56cb0d'], + }), + ('GenABEL.data', '1.0.0', { + 'checksums': ['2c28d5df63ae13545cf7aea6ce5f22ae1bbb58219fdaed6c1d5d5affc072c65c'], + }), + ('GenABEL', '1.8-0', { + 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch new file mode 100644 index 000000000000..037f9f5bc50c --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch @@ -0,0 +1,41 @@ +Replace the protobuf map files so that the required symbols are extern "C++" +Fix from https://github.com/protocolbuffers/protobuf/issues/5144#issuecomment-688723405 + +Add extra path to includes. + +Patch by Simon Branford (University of Birmingham) +--- RProtoBufLib/configure.orig 2021-06-05 10:58:25.972255000 +0100 ++++ RProtoBufLib/configure 2021-06-05 11:08:16.635526105 +0100 +@@ -2867,6 +2867,23 @@ + gzip -dc ${PBTGZNAME} | tar -xf - + fi; + ++mapfiles="libprotoc.map libprotobuf-lite.map libprotobuf.map" ++for mapfile in ${mapfiles}; do ++ cat << EOF > protobuf-3.13.0/src/${mapfile} ++{ ++ global: ++ extern "C++" { ++ *google*; ++ }; ++ scc_info_*; ++ descriptor_table_*; ++ ++ local: ++ *; ++}; ++EOF ++done ++ + #run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) + cd ${BASEPBNAME} + #./autogen.sh +--- RProtoBufLib/src/Makevars.in.orig 2021-06-05 11:58:07.587850000 +0100 ++++ RProtoBufLib/src/Makevars.in 2021-06-05 11:58:57.608744000 +0100 +@@ -1,5 +1,5 @@ + CXX_STD = CXX11 +-PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ ++PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ -I@PBBUILD@/src + #expose headers in installed package include folder + USER_INCLUDE = ${R_PACKAGE_DIR}/include + USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/