From bb7a5407c38cb8dd08e6b4896d8abc0c6a7f8012 Mon Sep 17 00:00:00 2001 From: Jay Hesselberth Date: Fri, 23 Feb 2024 12:13:32 -0700 Subject: [PATCH] update renv --- renv.lock | 1761 +++++++++++++++++++------------------------- renv/activate.R | 39 +- renv/settings.json | 2 +- 3 files changed, 786 insertions(+), 1016 deletions(-) diff --git a/renv.lock b/renv.lock index b7a1b889..b4f8474c 100644 --- a/renv.lock +++ b/renv.lock @@ -1,40 +1,40 @@ { "R": { - "Version": "4.3.1", + "Version": "4.3.2", "Repositories": [ { "Name": "BioCsoft", - "URL": "https://bioconductor.org/packages/3.17/bioc" + "URL": "https://bioconductor.org/packages/3.18/bioc" }, { "Name": "BioCann", - "URL": "https://bioconductor.org/packages/3.17/data/annotation" + "URL": "https://bioconductor.org/packages/3.18/data/annotation" }, { "Name": "BioCexp", - "URL": "https://bioconductor.org/packages/3.17/data/experiment" + "URL": "https://bioconductor.org/packages/3.18/data/experiment" }, { "Name": "BioCworkflows", - "URL": "https://bioconductor.org/packages/3.17/workflows" + "URL": "https://bioconductor.org/packages/3.18/workflows" }, { "Name": "BioCbooks", - "URL": "https://bioconductor.org/packages/3.17/books" + "URL": "https://bioconductor.org/packages/3.18/books" }, { "Name": "CRAN", - "URL": "https://packagemanager.posit.co/cran/latest" + "URL": "https://cran.rstudio.com" } ] }, "Bioconductor": { - "Version": "3.17" + "Version": "3.18" }, "Packages": { "AnnotationDbi": { "Package": "AnnotationDbi", - "Version": "1.62.2", + "Version": "1.64.1", "Source": "Bioconductor", "Requirements": [ "Biobase", @@ -49,11 +49,11 @@ "stats", "stats4" ], - "Hash": "e6c671413b55490c11402f78889384d9" + "Hash": "27587689922e22f60ec9ad0182a0a825" }, "AnnotationFilter": { "Package": "AnnotationFilter", - "Version": "1.24.0", + "Version": "1.26.0", "Source": "Bioconductor", "Requirements": [ "GenomicRanges", @@ -62,11 +62,11 @@ "methods", "utils" ], - "Hash": "5ee6a8b3d2ebe0eff2149c526dda4b64" + "Hash": "759acec0b1522c1a85c6ba703d4c0ec5" }, "AnnotationHub": { "Package": "AnnotationHub", - "Version": "3.8.0", + "Version": "3.10.0", "Source": "Bioconductor", "Requirements": [ "AnnotationDbi", @@ -86,21 +86,23 @@ "utils", "yaml" ], - 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"Version": "2.8.0", + "Version": "2.10.1", "Source": "Bioconductor", "Requirements": [ "DBI", @@ -164,11 +166,11 @@ "stats", "utils" ], - "Hash": "4fcebdf379954d5d1a3291006a93499b" + "Hash": "ac2a12468b948654220ed90ae94e9d08" }, "BiocGenerics": { "Package": "BiocGenerics", - "Version": "0.46.0", + "Version": "0.48.1", "Source": "Bioconductor", "Requirements": [ "R", @@ -177,11 +179,11 @@ "stats", "utils" ], - "Hash": "c179ae59955c36f5d0068ed29ce832f7" + "Hash": "e34278c65d7dffcc08f737bf0944ca9a" }, "BiocIO": { "Package": "BiocIO", - "Version": "1.10.0", + "Version": "1.12.0", "Source": "Bioconductor", "Requirements": [ "BiocGenerics", @@ -190,7 +192,7 @@ "methods", "tools" ], - "Hash": "a236af72143f9023b2f9f5f8baa81712" + "Hash": "aa543468283543c9a8dad23a4897be96" }, "BiocManager": { "Package": "BiocManager", @@ -204,8 +206,9 @@ }, "BiocNeighbors": { "Package": "BiocNeighbors", - "Version": "1.18.0", + "Version": "1.20.2", "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", "Requirements": [ "BiocParallel", "Matrix", @@ -215,11 +218,11 @@ "methods", "stats" ], - 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"Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -966,7 +972,7 @@ "Package": "RColorBrewer", "Version": "1.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -974,7 +980,7 @@ }, "RCurl": { "Package": "RCurl", - "Version": "1.98-1.12", + "Version": "1.98-1.14", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -982,7 +988,7 @@ "bitops", "methods" ], - "Hash": "1d6ed2d006d483f31c6d5531f3a39923" + "Hash": "47f648d288079d0c696804ad4e55197e" }, "ROCR": { "Package": "ROCR", @@ -1001,7 +1007,7 @@ }, "RSQLite": { "Package": "RSQLite", - "Version": "2.3.1", + "Version": "2.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1013,36 +1019,50 @@ "memoise", "methods", "pkgconfig", - "plogr" + "plogr", + "rlang" + ], + "Hash": "f5a75d57e0a3014a6ef537ac04a80fc6" + }, + "RSpectra": { + "Package": "RSpectra", + "Version": "0.16-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "Rcpp", + "RcppEigen" ], - 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"Version": "1.30.2", + "Version": "1.32.0", "Source": "Bioconductor", "Requirements": [ "Biobase", @@ -1343,7 +1393,7 @@ "tools", "utils" ], - "Hash": "6af56fbcb57deb9b094a352beee9a202" + "Hash": "caee529bf9710ff6fe1776612fcaa266" }, "TxDb.Hsapiens.UCSC.hg19.knownGene": { "Package": "TxDb.Hsapiens.UCSC.hg19.knownGene", @@ -1367,7 +1417,7 @@ }, "V8": { "Package": "V8", - "Version": "4.3.3", + "Version": "4.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1376,12 +1426,13 @@ "jsonlite", "utils" ], - "Hash": "20d81ec18bde233d8cc3265761fe8c93" + "Hash": "ca98390ad1cef2a5a609597b49d3d042" }, "VariantAnnotation": { "Package": "VariantAnnotation", - "Version": "1.46.0", + "Version": "1.48.1", "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", "Requirements": [ "AnnotationDbi", "BSgenome", @@ -1405,11 +1456,11 @@ "utils", "zlibbioc" ], - "Hash": "0370b868500a1e497628b238fa67d4fe" + "Hash": "a7500433dce48c27be8a34afe374c223" }, "XML": { "Package": "XML", - "Version": "3.99-0.14", + "Version": "3.99-0.16.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1417,11 +1468,11 @@ "methods", "utils" ], - 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"Version": "0.2.1", + "Version": "0.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1531,13 +1582,13 @@ "patchwork", "utils" ], - "Hash": "4c9386242f3196cbaac86d01f92e745e" + "Hash": "869a35e6d38fe9936eb578e09091842b" }, "askpass": { "Package": "askpass", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "sys" ], @@ -1570,7 +1621,7 @@ "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -1580,50 +1631,26 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], "Hash": "543776ae6848fde2f48ff3816d0628bc" }, - "basilisk": { - "Package": "basilisk", - "Version": "1.12.1", - "Source": "Bioconductor", - "Requirements": [ - 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"Version": "1.10.0", + "Version": "1.12.0", "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", "Requirements": [ "BiocNeighbors", "BiocParallel", @@ -1757,32 +1786,23 @@ "stats", "utils" ], - "Hash": "49d6795461d47f4c1a1d1d35ecc91b7a" - }, - "boot": { - "Package": "boot", - "Version": "1.3-28.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "graphics", - "stats" - ], - "Hash": "9a052fbcbe97a98ceb18dbfd30ebd96e" + "Hash": "fca0d5ffad6380f13cad4d7855107aef" }, "brio": { "Package": "brio", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "976cf154dfb043c012d87cddd8bca363" + "Requirements": [ + "R" + ], + "Hash": "68bd2b066e1fe780bbf62fc8bcc36de3" }, "broom": { "Package": "broom", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "backports", @@ -1799,11 +1819,32 @@ ], "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" }, + "broom.helpers": { + "Package": "broom.helpers", + "Version": "1.14.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "broom", + "cli", + "dplyr", + "labelled", + "lifecycle", + "purrr", + "rlang", + "stats", + "stringr", + "tibble", + "tidyr" + ], + "Hash": "ea30eb5d9412a4a5c2740685f680cd49" + }, "bslib": { "Package": "bslib", - "Version": "0.5.1", + "Version": "0.6.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "base64enc", @@ -1812,12 +1853,13 @@ "htmltools", "jquerylib", "jsonlite", + "lifecycle", "memoise", "mime", "rlang", "sass" ], - "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9" + "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" }, "caTools": { "Package": "caTools", @@ -1834,7 +1876,7 @@ "Package": "cachem", "Version": "1.0.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "fastmap", "rlang" @@ -1843,16 +1885,16 @@ }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "R6", "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "9f0e4fae4963ba775a5e5c520838c87b" }, "car": { "Package": "car", @@ -1892,7 +1934,7 @@ "Package": "cellranger", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "rematch", @@ -1902,7 +1944,7 @@ }, "checkmate": { "Package": "checkmate", - "Version": "2.2.0", + "Version": "2.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1910,11 +1952,11 @@ "backports", "utils" ], - "Hash": "ca9c113196136f4a9ca9ce6079c2c99e" + "Hash": "c01cab1cb0f9125211a6fc99d540e315" }, "circlize": { "Package": "circlize", - "Version": "0.4.15", + "Version": "0.4.16", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1929,24 +1971,24 @@ "stats", "utils" ], - "Hash": "2bb47a2fe6ab009b1dcc5566d8c3a988" + "Hash": "bf366c80e2b55a5383b4af8fa2a10b74" }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "utils" ], @@ -1966,23 +2008,9 @@ ], "Hash": "d6b53853800595408a776900bcc0c23f" }, - "cluster": { - "Package": "cluster", - "Version": "2.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats", - "utils" - ], - "Hash": "5edbbabab6ce0bf7900a74fd4358628e" - }, "clusterProfiler": { "Package": "clusterProfiler", - "Version": "4.8.3", + "Version": "4.10.0", "Source": "Bioconductor", "Requirements": [ "AnnotationDbi", @@ -1994,6 +2022,8 @@ "dplyr", "enrichplot", "gson", + "httr", + "igraph", "magrittr", "methods", "plyr", @@ -2004,11 +2034,11 @@ "utils", "yulab.utils" ], - "Hash": "358573de6d0ae89b2a9c27bb1f061898" + "Hash": "5a9a2580ce7435ba56af40279daa81ab" }, "clustifyr": { "Package": "clustifyr", - "Version": "1.12.0", + "Version": "1.14.0", "Source": "Bioconductor", "Requirements": [ "Matrix", @@ -2025,7 +2055,6 @@ "matrixStats", "methods", "proxy", - 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"Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Hash": "f7736a18de97dea803bde0a2daaafb27" }, "fastmatch": { @@ -2585,7 +2567,7 @@ }, "fgsea": { "Package": "fgsea", - "Version": "1.26.0", + "Version": "1.28.0", "Source": "Bioconductor", "Requirements": [ "BH", @@ -2602,14 +2584,17 @@ "stats", "utils" ], - "Hash": "62342298a29521147ea0764b22e8121e" + "Hash": "b2de43d04c504b819feec692e2b94523" }, "filelock": { "Package": "filelock", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "38ec653c2613bed60052ba3787bd8a2c" + "Requirements": [ + "R" + ], + "Hash": "192053c276525c8495ccfd523aa8f2d1" }, "fitdistrplus": { "Package": "fitdistrplus", @@ -2630,7 +2615,7 @@ "Package": "fontawesome", "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "htmltools", @@ -2642,7 +2627,7 @@ "Package": "forcats", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -2667,19 +2652,6 @@ ], "Hash": "618609b42c9406731ead03adf5379850" }, - "foreign": { - "Package": "foreign", - "Version": "0.8-85", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "stats", - "utils" - ], - "Hash": "26a24dde1722321b78f10d3bf42538d6" - }, "formatR": { "Package": "formatR", "Version": "1.14", @@ -2694,7 +2666,7 @@ "Package": "fs", "Version": "1.6.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "methods" @@ -2726,7 +2698,7 @@ }, "future": { "Package": "future", - "Version": "1.33.0", + "Version": "1.33.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2737,11 +2709,11 @@ "parallelly", "utils" ], - "Hash": "8e92c7bc53e91b9bb1faf9a6ef0e8514" + "Hash": "e57e292737f7a4efa9d8a91c5908222c" }, "future.apply": { "Package": "future.apply", - "Version": "1.11.0", + "Version": "1.11.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2751,13 +2723,13 @@ "parallel", "utils" ], - "Hash": "ba4be138fe47eac3e16a6deaa4da106e" + "Hash": "455e00c16ec193c8edcf1b2b522b3288" }, "gargle": { "Package": "gargle", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -2779,7 +2751,7 @@ "Package": "generics", "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "methods" @@ -2803,7 +2775,7 @@ }, "ggforce": { "Package": "ggforce", - "Version": "0.4.1", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2828,11 +2800,11 @@ "vctrs", "withr" ], - "Hash": "a06503f54e227f79b45a72df2946a2d2" + "Hash": "384b388bd9155468d2c851846ee69f9f" }, "ggfun": { "Package": "ggfun", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2843,23 +2815,23 @@ "rlang", "utils" ], - 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"Version": "0.5.4", + "Version": "0.5.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3000,7 +2972,7 @@ "scales", "withr" ], - "Hash": "c76ee8fe60939384b9726128e38caea0" + "Hash": "66488692cb8621bc78df1b9b819497a6" }, "ggsci": { "Package": "ggsci", @@ -3025,6 +2997,29 @@ ], "Hash": "a57f0f5dbcfd0d77ad4ff33032f5dc79" }, + "ggstats": { + "Package": "ggstats", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "broom.helpers", + "cli", + "dplyr", + "forcats", + "ggplot2", + "lifecycle", + "magrittr", + "patchwork", + "purrr", + "rlang", + "scales", + "stats", + "stringr", + "tidyr" + ], + "Hash": "006a64911e79a7dc7cbf839a57baaff4" + }, "ggtext": { "Package": "ggtext", "Version": "0.1.2", @@ -3042,7 +3037,7 @@ }, "ggthemes": { "Package": "ggthemes", - "Version": "4.2.4", + "Version": "5.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3050,17 +3045,18 @@ "ggplot2", "graphics", "grid", + "lifecycle", "methods", "purrr", "scales", "stringr", "tibble" ], - "Hash": "617fb2c300f68e8b1ba21043fba88fd7" + "Hash": "16a4974681fc751a09a1250431361896" }, "ggtree": { "Package": "ggtree", - "Version": "3.8.2", + "Version": "3.10.0", "Source": "Bioconductor", "Requirements": [ "R", @@ -3083,7 +3079,7 @@ "utils", "yulab.utils" ], - "Hash": "8959d04f88a175de3f0cd2b46b4c2a65" + "Hash": "f009cfa13d3884c01cc6300443e397eb" }, "globals": { "Package": "globals", @@ -3098,14 +3094,14 @@ }, "glue": { "Package": "glue", - "Version": "1.6.2", + "Version": "1.7.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "methods" ], - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" + "Hash": "e0b3a53876554bd45879e596cdb10a52" }, "goftest": { "Package": "goftest", @@ -3122,7 +3118,7 @@ "Package": "googledrive", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -3147,7 +3143,7 @@ "Package": "googlesheets4", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cellranger", @@ -3173,7 +3169,7 @@ }, "gplots": { "Package": "gplots", - "Version": "3.1.3", + "Version": "3.1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3184,11 +3180,11 @@ "methods", "stats" ], - "Hash": "75437dd4c43599f6e9418ea249495fda" + "Hash": "f72b5d1ed587f8905e38ee7295e88d80" }, "graphlayouts": { "Package": "graphlayouts", - "Version": "1.0.1", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3197,7 +3193,7 @@ "RcppArmadillo", "igraph" ], - "Hash": "5da48b0c093d8ac824e41255fb9ba197" + "Hash": "5e9e4cd284ff8abba3cfc43268e3ddd5" }, "gridExtra": { "Package": "gridExtra", @@ -3262,7 +3258,7 @@ }, "gt": { "Package": "gt", - "Version": "0.9.0", + "Version": "0.10.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3284,17 +3280,17 @@ "rlang", "sass", "scales", - "tibble", "tidyselect", + "vctrs", "xml2" ], - "Hash": "d55233a737e43e44987724e57dfec302" + "Hash": "03009c105dfae79460b8eb9d8cf791e4" }, "gtable": { "Package": "gtable", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -3307,7 +3303,7 @@ }, "gtools": { "Package": "gtools", - "Version": "3.9.4", + "Version": "3.9.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3315,13 +3311,13 @@ "stats", "utils" ], - "Hash": "88bb96eaf7140cdf29e374ef74182220" + "Hash": "588d091c35389f1f4a9d533c8d709b35" }, "haven": { "Package": "haven", - "Version": "2.5.3", + "Version": "2.5.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -3336,13 +3332,13 @@ "tidyselect", "vctrs" ], - "Hash": "9b302fe352f9cfc5dcf0a4139af3a565" + "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1" }, "here": { "Package": "here", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "rprojroot" ], @@ -3369,7 +3365,7 @@ "Package": "highr", "Version": "0.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "xfun" @@ -3380,7 +3376,7 @@ "Package": "hms", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "lifecycle", "methods", @@ -3392,10 +3388,11 @@ }, "htmlTable": { "Package": "htmlTable", - "Version": "2.4.1", + "Version": "2.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "checkmate", "htmltools", "htmlwidgets", @@ -3405,13 +3402,13 @@ "rstudioapi", "stringr" ], - "Hash": "d5b485330dcfe241b50db157bf898e97" + "Hash": "0164d8cade33fac2190703da7e6e3241" }, "htmltools": { "Package": "htmltools", - "Version": "0.5.6", + "Version": "0.5.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "base64enc", @@ -3422,11 +3419,11 @@ "rlang", "utils" ], - "Hash": "a2326a66919a3311f7fbb1e3bf568283" + "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.2", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3437,28 +3434,13 @@ "rmarkdown", "yaml" ], - "Hash": "a865aa85bcb2697f47505bfd70422471" - }, - "httpuv": { - "Package": "httpuv", - "Version": "1.6.11", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "Rcpp", - "later", - "promises", - "utils" - ], - "Hash": "838602f54e32c1a0f8cc80708cefcefa" + "Hash": "04291cc45198225444a397606810ac37" }, "httr": { "Package": "httr", "Version": "1.4.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "R6", @@ -3480,7 +3462,7 @@ "Package": "ids", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "openssl", "uuid" @@ -3489,7 +3471,7 @@ }, "igraph": { "Package": "igraph", - "Version": "1.5.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3505,13 +3487,14 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "80401cb5ec513e8ddc56764d03f63669" + "Hash": "e3baa015afa83d9f1b748db5a2aedb5a" }, "interactiveDisplayBase": { "Package": "interactiveDisplayBase", - "Version": "1.38.0", + "Version": "1.40.0", "Source": "Bioconductor", "Requirements": [ "BiocGenerics", @@ -3520,11 +3503,11 @@ "methods", "shiny" ], - "Hash": "bb387403478f98a8e1574f27d5bcfbcf" + "Hash": "776b86cd30211a590997dc15d02c8eff" }, "interp": { "Package": "interp", - "Version": "1.1-4", + "Version": "1.1-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3533,7 +3516,7 @@ "RcppEigen", "deldir" ], - "Hash": "3fff1eabca2e23beba50982e9b6fccaa" + "Hash": "824328a500468b76e61402b2cb3033df" }, "irlba": { "Package": "irlba", @@ -3552,7 +3535,7 @@ "Package": "isoband", "Version": "0.2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "grid", "utils" @@ -3606,7 +3589,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "htmltools" ], @@ -3614,13 +3597,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.7", + "Version": "1.8.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "methods" ], - "Hash": "266a20443ca13c65688b2116d5220f76" + "Hash": "e1b9c55281c5adc4dd113652d9e26768" }, "juicyjuice": { "Package": "juicyjuice", @@ -3634,9 +3617,9 @@ }, "knitr": { "Package": "knitr", - "Version": "1.44", + "Version": "1.45", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "evaluate", @@ -3646,44 +3629,50 @@ "xfun", "yaml" ], - "Hash": "60885b9f746c9dfaef110d070b5f7dc0" + "Hash": "1ec462871063897135c1bcbe0fc8f07d" }, "labeling": { "Package": "labeling", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "graphics", "stats" ], "Hash": "b64ec208ac5bc1852b285f665d6368b3" }, - "lambda.r": { - "Package": "lambda.r", - "Version": "1.2.4", + "labelled": { + "Package": "labelled", + "Version": "2.12.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "formatR" + "dplyr", + "haven", + "lifecycle", + "rlang", + "stringr", + "tidyr", + "vctrs" ], - "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" + "Hash": "1ec27c624ece6c20431e9249bd232797" }, - "later": { - "Package": "later", - "Version": "1.3.1", + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "Rcpp", - "rlang" + "R", + "formatR" ], - "Hash": "40401c9cf2bc2259dfe83311c9384710" + "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" }, "lattice": { "Package": "lattice", - "Version": "0.21-8", + "Version": "0.21-9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3694,7 +3683,7 @@ "stats", "utils" ], - "Hash": "0b8a6d63c8770f02a8b5635f3c431e6b" + "Hash": "5558c61e0136e247252f5f952cdaad6a" }, "latticeExtra": { "Package": "latticeExtra", @@ -3728,57 +3717,58 @@ }, "leiden": { "Package": "leiden", - "Version": "0.4.3", + "Version": "0.4.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "igraph", "methods", "reticulate" ], - "Hash": "3ddd87b156152001d3ab82979808af00" + "Hash": "b21c4ae2bb7935504c42bcdf749c04e6" }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" + "Hash": "b8552d117e1b808b09a832f589b79035" }, "limma": { "Package": "limma", - "Version": "3.56.2", + "Version": "3.58.1", "Source": "Bioconductor", "Requirements": [ "R", "grDevices", "graphics", "methods", + "statmod", "stats", "utils" ], - "Hash": "15b74284b9eb4641fa99a01e445a8256" + "Hash": "74c3b64358e0be7edc3ecd130816dd3f" }, "listenv": { "Package": "listenv", - "Version": "0.9.0", + "Version": "0.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "4fbd3679ec8ee169ba28d4b1ea7d0e8f" + "Hash": "e2fca3e12e4db979dccc6e519b10a7ee" }, "lme4": { "Package": "lme4", - "Version": "1.1-34", + "Version": "1.1-35.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3800,7 +3790,7 @@ "stats", "utils" ], - "Hash": "73ed88b282d27d4cf3d89b744aa21217" + "Hash": "07fb0c5b727b15b0ce40feb641498e4e" }, "lmtest": { "Package": "lmtest", @@ -3830,7 +3820,7 @@ "Package": "lubridate", "Version": "1.9.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "generics", @@ -3841,7 +3831,7 @@ }, "magick": { "Package": "magick", - "Version": "2.8.0", + "Version": "2.8.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3849,13 +3839,13 @@ "curl", "magrittr" ], - "Hash": "88a1be45614781633df69ab666d66143" + "Hash": "3f6bcbb8a0c1c9365b2f02d5d04ad7bc" }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -3863,32 +3853,32 @@ }, "markdown": { "Package": "markdown", - "Version": "1.8", + "Version": "1.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "commonmark", "utils", "xfun" ], - "Hash": "93cecf1e5f828d0fc1605a00ad48e3a2" + "Hash": "765cf53992401b3b6c297b69e1edb8bd" }, "matrixStats": { "Package": "matrixStats", - "Version": "1.0.0", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "9143629fd64335aac6a6250d1c1ed82a" + "Hash": "33a3ca9e732b57244d14f5d732ffc9eb" }, "memoise": { "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "cachem", "rlang" @@ -3897,12 +3887,13 @@ }, "metapod": { "Package": "metapod", - "Version": "1.8.0", + "Version": "1.10.1", "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", "Requirements": [ "Rcpp" ], - "Hash": "577022e3e4c4d3a3c812aefbe640467e" + "Hash": "64e76c256313f40ff540e371e58b5503" }, "mgcv": { "Package": "mgcv", @@ -3925,24 +3916,12 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "tools" ], "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, - "miniUI": { - "Package": "miniUI", - "Version": "0.1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "htmltools", - "shiny", - "utils" - ], - "Hash": "fec5f52652d60615fdb3957b3d74324a" - }, "minqa": { "Package": "minqa", "Version": "1.2.6", @@ -3957,7 +3936,7 @@ "Package": "modelr", "Version": "0.1.11", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "broom", @@ -3991,7 +3970,7 @@ "Package": "munsell", "Version": "0.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "colorspace", "methods" @@ -4022,18 +4001,6 @@ ], "Hash": "277c67a08f358f42b6a77826e4492f79" }, - "nnet": { - "Package": "nnet", - "Version": "7.3-19", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "2c797b46eea7fb58ede195bc0b1f1138" - }, "numDeriv": { "Package": "numDeriv", "Version": "2016.8-1.1", @@ -4048,7 +4015,7 @@ "Package": "openssl", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "askpass" ], @@ -4056,14 +4023,14 @@ }, "org.Hs.eg.db": { "Package": "org.Hs.eg.db", - "Version": "3.17.0", + "Version": "3.18.0", "Source": "Bioconductor", "Requirements": [ "AnnotationDbi", "R", "methods" ], - "Hash": "bc5b9e048c58ce45bb646c10d311d1e2" + "Hash": "120d734b7c6eaed99d8f5f61e6c125ed" }, "palmerpenguins": { "Package": "palmerpenguins", @@ -4077,7 +4044,7 @@ }, "parallelly": { "Package": "parallelly", - "Version": "1.36.0", + "Version": "1.37.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4085,11 +4052,11 @@ "tools", "utils" ], - "Hash": "bca377e1c87ec89ebed77bba00635b2e" + "Hash": "8da17de8b15c89b574269fc414ff4e20" }, "patchwork": { "Package": "patchwork", - "Version": "1.1.3", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4103,7 +4070,7 @@ "stats", "utils" ], - "Hash": "c5754106c02e8e019941100c81149431" + "Hash": "9c8ab14c00ac07e9e04d1664c0b74486" }, "pbapply": { "Package": "pbapply", @@ -4155,7 +4122,7 @@ "Package": "pillar", "Version": "1.9.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "cli", "fansi", @@ -4168,55 +4135,16 @@ ], "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, - "pkgbuild": { - "Package": "pkgbuild", - "Version": "1.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "callr", - "cli", - "crayon", - "desc", - "prettyunits", - "processx", - "rprojroot" - ], - "Hash": "beb25b32a957a22a5c301a9e441190b3" - }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "utils" ], "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, - "pkgload": { - "Package": "pkgload", - "Version": "1.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "crayon", - "desc", - "fs", - "glue", - "methods", - "pkgbuild", - "rlang", - "rprojroot", - "utils", - "withr" - ], - "Hash": "903d68319ae9923fb2e2ee7fa8230b91" - }, "plogr": { "Package": "plogr", "Version": "0.2.0", @@ -4226,7 +4154,7 @@ }, "plotly": { "Package": "plotly", - "Version": "4.10.2", + "Version": "4.10.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4254,18 +4182,18 @@ "vctrs", "viridisLite" ], - "Hash": "6c00a09ba7d34917d9a3e28b15dd74e3" + "Hash": "a1ac5c03ad5ad12b9d1597e00e23c3dd" }, "plyr": { "Package": "plyr", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "Rcpp" ], - "Hash": "d744387aef9047b0b48be2933d78e862" + "Hash": "6b8177fd19982f0020743fadbfdbd933" }, "png": { "Package": "png", @@ -4298,75 +4226,32 @@ ], "Hash": "ceb5c2a59ba33d42d051285a3e8a5118" }, - "praise": { - "Package": "praise", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a555924add98c99d2f411e37e7d25e9f" - }, - "presto": { - "Package": "presto", - "Version": "1.0.0", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteRepo": "presto", - "RemoteUsername": "immunogenomics", - "RemoteRef": "HEAD", - "RemoteSha": "31dc97fed5e2e7fc323ae4af62f72181cc51d9a3", - "Requirements": [ - "Matrix", - "R", - "Rcpp", - "RcppArmadillo", - "data.table", - "dplyr", - "methods", - "purrr", - "rlang", - "stats", - "tibble", - "tidyr", - "utils" - ], - "Hash": "d3fa552970edc057bd8b4e00e6c60bdf" - }, - "prettyunits": { - 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"Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "Rcpp", - "fastmap", - "later", - "magrittr", - "rlang", - "stats" - ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" - }, "proxy": { "Package": "proxy", "Version": "0.4-27", @@ -4410,25 +4279,20 @@ }, "ps": { "Package": "ps", - "Version": "1.7.5", + "Version": "1.7.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "utils" ], - "Hash": "709d852d33178db54b17c722e5b1e594" + "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" }, "purrr": { "Package": "purrr", - "Version": "1.0.2.9000", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteRepo": "purrr", - "RemoteUsername": "tidyverse", - "RemoteRef": "HEAD", - "RemoteSha": "ac4f5a9b9ff2b5b36770c4c5e064547264544fd2", + "Version": "1.0.2", + "Source": "Repository", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -4437,7 +4301,7 @@ "rlang", "vctrs" ], - "Hash": "dff662ed13d68d319653b540040fe72f" + "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" }, "quantreg": { "Package": "quantreg", @@ -4459,7 +4323,7 @@ }, "qvalue": { "Package": "qvalue", - "Version": "2.32.0", + "Version": "2.34.0", "Source": "Bioconductor", "Requirements": [ "R", @@ -4468,11 +4332,11 @@ "reshape2", "splines" ], - "Hash": "d07f7cf42c6415334ebc6867b6eed588" + "Hash": "76fc42834c44b69e4021f6ade524d299" }, "rGADEM": { "Package": "rGADEM", - "Version": "2.48.0", + "Version": "2.50.0", "Source": "Bioconductor", "Requirements": [ "BSgenome", @@ -4484,24 +4348,24 @@ "methods", "seqLogo" ], - "Hash": "856098ada2db5829b008294febc2e287" + "Hash": "6dad0172698273a1250a9289c44e412b" }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" + "Hash": "90a1b8b7e518d7f90480d56453b4d062" }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -4509,13 +4373,13 @@ }, "reactR": { "Package": "reactR", - "Version": "0.4.4", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "htmltools" ], - "Hash": "75389c8091eb14ee21c6bc87a88b3809" + "Hash": "c9014fd1a435b2d790dd506589cb24e5" }, "reactable": { "Package": "reactable", @@ -4534,9 +4398,9 @@ }, "readr": { "Package": "readr", - "Version": "2.1.4", + "Version": "2.1.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "R6", @@ -4553,13 +4417,13 @@ "utils", "vroom" ], - "Hash": "b5047343b3825f37ad9d3b5d89aa1078" + "Hash": "9de96463d2117f6ac49980577939dfb3" }, "readxl": { "Package": "readxl", "Version": "1.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cellranger", @@ -4572,7 +4436,7 @@ }, "regioneR": { "Package": "regioneR", - 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"Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -5298,13 +5112,13 @@ "stats", "utils" ], - "Hash": "cf3a811e9a8ce9feff6c5b89209ed520" + "Hash": "d05f37e83177665a5eb466da953ffc0f" }, "spatstat.sparse": { "Package": "spatstat.sparse", - "Version": "3.0-2", + "Version": "3.0-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "Matrix", "R", @@ -5315,13 +5129,13 @@ "tensor", "utils" ], - "Hash": "82a7d5a77f165b08dae877ef98dc6fcc" + "Hash": "1daaecefd754bb259a5ad5ce95a2cdcc" }, "spatstat.utils": { "Package": "spatstat.utils", - "Version": "3.0-3", + "Version": "3.0-4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -5330,7 +5144,7 @@ "stats", "utils" ], - "Hash": "8f9764a85e3ca99604625f7ab6012418" + "Hash": "81d929f43f8532c1f8180a105449d414" }, "statmod": { "Package": "statmod", @@ -5346,22 +5160,22 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.8.3", "Source": "Repository", - 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"Hash": "1ab6223d3670fac7143202cb6a2d43d5" + "Hash": "997aac9ad649e0ef3b97f96cddd5622b" }, "tibble": { "Package": "tibble", "Version": "3.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "fansi", @@ -5478,7 +5246,7 @@ }, "tidygraph": { "Package": "tidygraph", - "Version": "1.2.3", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5487,6 +5255,7 @@ "cpp11", "dplyr", "igraph", + "lifecycle", "magrittr", "pillar", "rlang", @@ -5496,13 +5265,13 @@ "tools", "utils" ], - "Hash": "0fc97a52b4b32a0b4a3de4c5241348e2" + "Hash": "2149824d406f233b57b087be72c5f163" }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -5519,13 +5288,13 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -5539,7 +5308,7 @@ }, "tidytree": { "Package": "tidytree", - "Version": "0.4.5", + "Version": "0.4.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5557,13 +5326,13 @@ "tidyselect", "yulab.utils" ], - "Hash": "b6c0b32b3632419e1a91bf4e0c4f7337" + "Hash": "a700d295c0eff82fbce42eac067bb89d" }, "tidyverse": { "Package": "tidyverse", "Version": "2.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "broom", @@ -5601,43 +5370,50 @@ }, "timechange": { "Package": "timechange", - "Version": "0.2.0", + "Version": "0.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cpp11" ], - "Hash": "8548b44f79a35ba1791308b61e6012d7" + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" }, "tinytex": { "Package": "tinytex", - "Version": "0.46", + "Version": "0.49", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "xfun" ], - "Hash": "0c41a73214d982f539c56a7773c7afa5" + "Hash": "5ac22900ae0f386e54f1c307eca7d843" }, "treeio": { "Package": "treeio", - "Version": "1.24.3", - "Source": "Bioconductor", + "Version": "1.27.0.002", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "GuangchuangYu", + "RemoteRepo": "treeio", + "RemoteRef": "devel", + "RemoteSha": "f6686330e437867add5dc80ef2e5db85c866c6c3", "Requirements": [ "R", "ape", - "cli", "dplyr", "jsonlite", "magrittr", "methods", "rlang", + "stats", "tibble", "tidytree", - "utils" + "utils", + "yulab.utils" ], - "Hash": "c8c8efbcec2f1512d6079af62b0f112b" + "Hash": "545643f9a451c86eea21504c2ac59b3b" }, "tweenr": { "Package": "tweenr", @@ -5656,20 +5432,20 @@ }, "tximport": { "Package": "tximport", - "Version": "1.28.0", + "Version": "1.30.0", "Source": "Bioconductor", "Requirements": [ "methods", "stats", "utils" ], - "Hash": "3d62da58bb159033cfcc02ac7b9cf834" + "Hash": "6e9621b0f1bf9398255f32c7000a7e16" }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cpp11" @@ -5678,23 +5454,23 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "uuid": { "Package": "uuid", - "Version": "1.1-1", + "Version": "1.2-0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], - "Hash": "3d78edfb977a69fc7a0341bee25e163f" + "Hash": "303c19bfd970bece872f93a824e323d9" }, "uwot": { "Package": "uwot", @@ -5736,9 +5512,9 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.6.3", + "Version": "0.6.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "cli", @@ -5746,23 +5522,23 @@ "lifecycle", "rlang" ], - "Hash": "d0ef2856b83dc33ea6e255caf6229ee2" + "Hash": "c03fa420630029418f7e6da3667aac4a" }, "vipor": { "Package": "vipor", - "Version": "0.4.5", + "Version": "0.4.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "graphics", "stats" ], - "Hash": "ea85683da7f2bfa63a98dc6416892591" + "Hash": "86493c62c14eb78140f1725003958a77" }, "viridis": { "Package": "viridis", - "Version": "0.6.4", + "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5771,13 +5547,13 @@ "gridExtra", "viridisLite" ], - "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1" + "Hash": "acd96d9fa70adeea4a5a1150609b9745" }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R" ], @@ -5803,9 +5579,9 @@ }, "vroom": { "Package": "vroom", - "Version": "1.6.3", + "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "bit64", @@ -5825,82 +5601,55 @@ "vctrs", "withr" ], - "Hash": "8318e64ffb3a70e652494017ec455561" - }, - "waldo": { - "Package": "waldo", - "Version": "0.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cli", - "diffobj", - "fansi", - "glue", - "methods", - "rematch2", - "rlang", - "tibble" - ], - "Hash": "2c993415154cdb94649d99ae138ff5e5" + "Hash": "390f9315bc0025be03012054103d227c" }, "withr": { "Package": "withr", - "Version": "2.5.1", + "Version": "3.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", "grDevices", - "graphics", - "stats" + "graphics" ], - "Hash": "d77c6f74be05c33164e33fbc85540cae" + "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" }, "xfun": { "Package": "xfun", - "Version": "0.40", + "Version": "0.42", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ + "grDevices", "stats", "tools" ], - "Hash": "be07d23211245fc7d4209f54c4e4ffc8" + "Hash": "fd1349170df31f7a10bd98b0189e85af" }, "xml2": { "Package": "xml2", - "Version": "1.3.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "6c40e5cfcc6aefd88110666e18c31f40" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", + "Version": "1.3.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://packagemanager.posit.co/cran/latest", "Requirements": [ "R", - "stats", - "utils" + "cli", + "methods", + "rlang" ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.8", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + "Repository": "https://packagemanager.posit.co/cran/latest", + "Hash": "29240487a071f535f5e5d5a323b7afbd" }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.1.0", + "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -5913,13 +5662,13 @@ "tools", "utils" ], - "Hash": "792b3c5bc98f04a7d49cbd8c55fe0770" + "Hash": "60ee2aaa179dc282e9fa7367bad76e89" }, "zlibbioc": { "Package": "zlibbioc", - "Version": "1.46.0", + "Version": "1.48.0", "Source": "Bioconductor", - "Hash": "20158ef5adb641f0b4e8d63136f0e870" + "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911" }, "zoo": { "Package": "zoo", diff --git a/renv/activate.R b/renv/activate.R index cb5401f9..d98ed734 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.4" attr(version, "sha") <- NULL # the project directory @@ -31,6 +31,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -50,9 +58,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -1041,7 +1062,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1050,7 +1071,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1063,14 +1084,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -1118,14 +1139,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -1152,7 +1173,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } diff --git a/renv/settings.json b/renv/settings.json index 906b13bc..45ee56fb 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -1,5 +1,5 @@ { - "bioconductor.version": "3.17", + "bioconductor.version": "3.18", "external.libraries": [], "ignored.packages": [], "package.dependency.fields": [