From dd252a29c11f9ea54b1c3f8f1856e864040cc834 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 22 Nov 2023 15:20:02 -0500 Subject: [PATCH 1/2] Update renv & python --- .pre-commit-config.yaml | 1 + docker/renv.lock | 356 +++++++++++++++++++++++++--------------- docker/requirements.txt | 10 +- renv/activate.R | 27 +-- 4 files changed, 230 insertions(+), 164 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 34cae75d..280f85c3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,6 +36,7 @@ repos: (.*/|)NAMESPACE| (.*/|)renv/settings\.dcf| (.*/|)renv\.lock| + (.*/|)requirements\.txt| (.*/|)WORDLIST| \.github/workflows/.*| data/.*| diff --git a/docker/renv.lock b/docker/renv.lock index 35dd0bd6..99856683 100644 --- a/docker/renv.lock +++ b/docker/renv.lock @@ -323,7 +323,7 @@ }, "DT": { "Package": "DT", - "Version": "0.29", + "Version": "0.30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -336,7 +336,7 @@ "magrittr", "promises" ], - "Hash": "02f42b77a951a5ea7c891ef5c187d774" + "Hash": "dffb4d94a00be1b4a4507e53ab95bd90" }, "DelayedArray": { "Package": "DelayedArray", @@ -431,8 +431,9 @@ }, "GenomeInfoDb": { "Package": "GenomeInfoDb", - "Version": "1.36.3", + "Version": "1.36.4", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "BiocGenerics", "GenomeInfoDbData", @@ -445,7 +446,7 @@ "stats4", "utils" ], - "Hash": "7e59ef611ff4e9014ed59d3998aa34e4" + "Hash": "1c6756527d78e8135d34662d2e1d54ec" }, "GenomeInfoDbData": { "Package": "GenomeInfoDbData", @@ -507,8 +508,9 @@ }, "GenomicRanges": { "Package": "GenomicRanges", - "Version": "1.52.0", + "Version": "1.52.1", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "BiocGenerics", "GenomeInfoDb", @@ -521,7 +523,7 @@ "stats4", "utils" ], - "Hash": "dc2970e434666341650a7983435597bf" + "Hash": "c9471497a07953ded9b8889879c079e9" }, "GetoptLong": { "Package": "GetoptLong", @@ -588,8 +590,9 @@ }, "KEGGREST": { "Package": "KEGGREST", - "Version": "1.40.0", + "Version": "1.40.1", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "Biostrings", "R", @@ -597,7 +600,7 @@ "methods", "png" ], - "Hash": "b5a4bf06281c694bc38412812c70b011" + "Hash": "2988b310648d92e9d5c877d627068b9d" }, "KernSmooth": { "Package": "KernSmooth", @@ -627,7 +630,7 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1.1", + "Version": "1.6-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -640,7 +643,7 @@ "stats", "utils" ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" + "Hash": "1d1b6901cf9b6b1b446bc56a7d47efa4" }, "MatrixGenerics": { "Package": "MatrixGenerics", @@ -687,7 +690,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.2", + "Version": "2.12.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -698,7 +701,7 @@ "tools", "utils" ], - "Hash": "325f01db13da12c04d8f6e7be36ff514" + "Hash": "3dc2829b790254bfba21e60965787651" }, "R6": { "Package": "R6", @@ -729,7 +732,7 @@ }, "RCurl": { "Package": "RCurl", - "Version": "1.98-1.12", + "Version": "1.98-1.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -737,7 +740,7 @@ "bitops", "methods" ], - "Hash": "1d6ed2d006d483f31c6d5531f3a39923" + "Hash": "318c7b8d68358b45cbc6115dda23d7db" }, "ROCR": { "Package": "ROCR", @@ -756,7 +759,7 @@ }, "RSQLite": { "Package": "RSQLite", - "Version": "2.3.1", + "Version": "2.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -770,7 +773,20 @@ "pkgconfig", "plogr" ], - "Hash": "207c90cd5438a1f596da2cd54c606fee" + "Hash": "3de9b130745b42015c060758cf6d9b8d" + }, + "RSpectra": { + "Package": "RSpectra", + "Version": "0.16-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "Rcpp", + "RcppEigen" + ], + "Hash": "6b5ab997fd5ff6d46a5f1d9f8b76961c" }, "Rcpp": { "Package": "Rcpp", @@ -797,7 +813,7 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.6.4.0", + "Version": "0.12.6.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -807,32 +823,31 @@ "stats", "utils" ], - "Hash": "cafeccdc6577a445a15ce98b6a1805cf" + "Hash": "aabc6cb0f0953d0442d3c82d8a9d2610" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.3", + "Version": "0.3.3.9.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "Matrix", "R", "Rcpp", "stats", "utils" ], - "Hash": "1e035db628cefb315c571202d70202fe" + "Hash": "acb0a5bf38490f26ab8661b467f4f53a" }, "RcppHNSW": { "Package": "RcppHNSW", - "Version": "0.4.1", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp", "methods" ], - "Hash": "a3fd7fda39fec57a7086b4fb9fa8aba3" + "Hash": "6af2d9ed44e0281f6ae77eb6bed7a3c9" }, "RcppML": { "Package": "RcppML", @@ -972,8 +987,9 @@ }, "S4Vectors": { "Package": "S4Vectors", - "Version": "0.38.1", + "Version": "0.38.2", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "BiocGenerics", "R", @@ -982,7 +998,7 @@ "stats4", "utils" ], - "Hash": "f0a46e23a2a7d6aa27e945faf7f242c7" + "Hash": "338207894998073e7823706f886a1386" }, "ScaledMatrix": { "Package": "ScaledMatrix", @@ -998,7 +1014,7 @@ }, "Seurat": { "Package": "Seurat", - "Version": "4.4.0", + "Version": "5.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1009,17 +1025,21 @@ "RANN", "RColorBrewer", "ROCR", + "RSpectra", "Rcpp", "RcppAnnoy", "RcppEigen", + "RcppHNSW", "RcppProgress", "Rtsne", "SeuratObject", "cluster", "cowplot", + "fastDummies", "fitdistrplus", "future", "future.apply", + "generics", "ggplot2", "ggrepel", "ggridges", @@ -1032,6 +1052,7 @@ "irlba", "jsonlite", "leiden", + "lifecycle", "lmtest", "matrixStats", "methods", @@ -1056,11 +1077,11 @@ "utils", "uwot" ], - "Hash": "622e2dca3e48ed689fd418bffc0dc34e" + "Hash": "7529b4701d0ad499db7bbf4e6934aed0" }, "SeuratObject": { "Package": "SeuratObject", - "Version": "4.1.4", + "Version": "5.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1070,17 +1091,20 @@ "RcppEigen", "future", "future.apply", + "generics", "grDevices", "grid", + "lifecycle", "methods", "progressr", "rlang", "sp", + "spam", "stats", "tools", "utils" ], - "Hash": "1548d1c211c0a2eff1771991d4f71a9d" + "Hash": "424c2b9e50b053c86fc38f17e09917da" }, "SingleCellExperiment": { "Package": "SingleCellExperiment", @@ -1145,7 +1169,7 @@ }, "XML": { "Package": "XML", - "Version": "3.99-0.14", + "Version": "3.99-0.15", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1153,7 +1177,7 @@ "methods", "utils" ], - "Hash": "e5c8af79df616c135b21eaeb1dc6bc5c" + "Hash": "5ede9ddd092f132c14ca0b6799224cc0" }, "XVector": { "Package": "XVector", @@ -1535,7 +1559,7 @@ }, "clue": { "Package": "clue", - "Version": "0.3-64", + "Version": "0.3-65", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1545,7 +1569,7 @@ "methods", "stats" ], - "Hash": "f013e45eb656a4bb17b39cb24827a51f" + "Hash": "d6b53853800595408a776900bcc0c23f" }, "cluster": { "Package": "cluster", @@ -1659,13 +1683,13 @@ }, "curl": { "Package": "curl", - "Version": "5.0.2", + "Version": "5.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "511bacbfa153a15251166b463b4da4f9" + "Hash": "9123f3ef96a2c1a93927d828b2fe7d4c" }, "data.table": { "Package": "data.table", @@ -1680,7 +1704,7 @@ }, "dbplyr": { "Package": "dbplyr", - "Version": "2.3.3", + "Version": "2.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1704,7 +1728,7 @@ "vctrs", "withr" ], - "Hash": "d6fd1b1440c1cacc6623aaa4e9fe352b" + "Hash": "59351f28a81f0742720b85363c4fdd61" }, "deldir": { "Package": "deldir", @@ -1795,9 +1819,19 @@ ], "Hash": "451e5edf411987991ab6a5410c45011f" }, + "dotCall64": { + "Package": "dotCall64", + "Version": "1.1-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "7744a30055fea449fc7cd98323b5887c" + }, "dplyr": { "Package": "dplyr", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1816,7 +1850,7 @@ "utils", "vctrs" ], - "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949" + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, "dqrng": { "Package": "dqrng", @@ -1909,8 +1943,9 @@ }, "ensembldb": { "Package": "ensembldb", - "Version": "2.24.0", + "Version": "2.24.1", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "AnnotationDbi", "AnnotationFilter", @@ -1931,22 +1966,22 @@ "methods", "rtracklayer" ], - "Hash": "cb99874dc074ad29fc691be022bb5974" + "Hash": "f94758e1925ab9ec977d8863498716c6" }, "evaluate": { "Package": "evaluate", - "Version": "0.21", + "Version": "0.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "d59f3b464e8da1aef82dc04b588b8dfb" + "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1954,7 +1989,7 @@ "grDevices", "utils" ], - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" + "Hash": "3e8583a60163b4bc1a80016e63b9959e" }, "farver": { "Package": "farver", @@ -1963,6 +1998,19 @@ "Repository": "CRAN", "Hash": "8106d78941f34855c440ddb946b8f7a5" }, + "fastDummies": { + "Package": "fastDummies", + "Version": "1.7.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "data.table", + "stringr", + "tibble" + ], + "Hash": "e0f9c0c051e0e8d89996d7f0c400539f" + }, "fastmap": { "Package": "fastmap", "Version": "1.1.1", @@ -2185,13 +2233,13 @@ }, "getopt": { "Package": "getopt", - "Version": "1.20.3", + "Version": "1.20.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "stats" ], - "Hash": "ad68e3263f0bc9269aab8c2039440117" + "Hash": "ed33b16c6d24f7ced1d68877ac2509ee" }, "ggbeeswarm": { "Package": "ggbeeswarm", @@ -2280,7 +2328,7 @@ }, "ggrepel": { "Package": "ggrepel", - "Version": "0.9.3", + "Version": "0.9.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2292,7 +2340,7 @@ "scales", "withr" ], - "Hash": "92edfac53774706b4d6099f3ee6f6306" + "Hash": "e9839af82cc43fda486a638b68b439b2" }, "ggridges": { "Package": "ggridges", @@ -2466,7 +2514,7 @@ }, "harmony": { "Package": "harmony", - "Version": "1.0.3", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2483,7 +2531,7 @@ "rlang", "tibble" ], - "Hash": "ae92e686936589dec53b0514cff659f6" + "Hash": "b223279a4daf22158de67a070ffebafa" }, "haven": { "Package": "haven", @@ -2543,7 +2591,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.6", + "Version": "0.5.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2556,7 +2604,7 @@ "rlang", "utils" ], - "Hash": "a2326a66919a3311f7fbb1e3bf568283" + "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -2575,7 +2623,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.11", + "Version": "1.6.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2586,7 +2634,7 @@ "promises", "utils" ], - "Hash": "838602f54e32c1a0f8cc80708cefcefa" + "Hash": "c992f75861325961c29a188b45e549f7" }, "httr": { "Package": "httr", @@ -2741,7 +2789,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.44", + "Version": "1.45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2753,7 +2801,7 @@ "xfun", "yaml" ], - "Hash": "60885b9f746c9dfaef110d070b5f7dc0" + "Hash": "1ec462871063897135c1bcbe0fc8f07d" }, "labeling": { "Package": "labeling", @@ -2790,7 +2838,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.21-8", + "Version": "0.22-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2801,7 +2849,7 @@ "stats", "utils" ], - "Hash": "0b8a6d63c8770f02a8b5635f3c431e6b" + "Hash": "7c5e89f04e72d6611c77451f6331a091" }, "lazyeval": { "Package": "lazyeval", @@ -2815,7 +2863,7 @@ }, "leiden": { "Package": "leiden", - "Version": "0.4.3", + "Version": "0.4.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2824,11 +2872,11 @@ "methods", "reticulate" ], - "Hash": "3ddd87b156152001d3ab82979808af00" + "Hash": "b21c4ae2bb7935504c42bcdf749c04e6" }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2837,7 +2885,7 @@ "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" + "Hash": "b8552d117e1b808b09a832f589b79035" }, "limma": { "Package": "limma", @@ -2907,7 +2955,7 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.9.2", + "Version": "1.9.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2916,7 +2964,7 @@ "methods", "timechange" ], - "Hash": "e25f18436e3efd42c7c590a1c4c15390" + "Hash": "680ad542fbcf801442c83a6ac5a2126c" }, "magrittr": { "Package": "magrittr", @@ -2930,13 +2978,13 @@ }, "matrixStats": { "Package": "matrixStats", - "Version": "1.0.0", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "9143629fd64335aac6a6250d1c1ed82a" + "Hash": "68d317093459a3f0852b1dd52d9e1ea6" }, "memoise": { "Package": "memoise", @@ -3129,13 +3177,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "273a6bb4a9844c296a459d2176673270" + "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" }, "optparse": { "Package": "optparse", @@ -3231,6 +3279,24 @@ ], "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", @@ -3243,7 +3309,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2.1", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3254,12 +3320,13 @@ "fs", "glue", "methods", + "pkgbuild", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "a7f498a1b2a4a6816148e498509f6e1d" + "Hash": "903d68319ae9923fb2e2ee7fa8230b91" }, "plogr": { "Package": "plogr", @@ -3270,7 +3337,7 @@ }, "plotly": { "Package": "plotly", - "Version": "4.10.2", + "Version": "4.10.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3298,18 +3365,18 @@ "vctrs", "viridisLite" ], - "Hash": "6c00a09ba7d34917d9a3e28b15dd74e3" + "Hash": "56914cc61df53f2d0283d5498680867e" }, "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", @@ -3323,13 +3390,13 @@ }, "polyclip": { "Package": "polyclip", - "Version": "1.10-4", + "Version": "1.10-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "66bbfa06f78108ee967220643596c91e" + "Hash": "436542aadb70675e361cf359285af7c7" }, "praise": { "Package": "praise", @@ -3340,10 +3407,13 @@ }, "prettyunits": { "Package": "prettyunits", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "95ef9167b75dde9d2ccc3c7528393e7e" + "Requirements": [ + "R" + ], + "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" }, "processx": { "Package": "processx", @@ -3440,14 +3510,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" + "Hash": "6ba2fa8740abdc2cc148407836509901" }, "rappdirs": { "Package": "rappdirs", @@ -3516,13 +3586,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "4b22ac016fe54028b88d0c68badbd061" + "Hash": "41b847654f567341725473431dd0d5ab" }, "reprex": { "Package": "reprex", @@ -3577,7 +3647,7 @@ }, "reticulate": { "Package": "reticulate", - "Version": "1.32.0", + "Version": "1.34.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3595,7 +3665,7 @@ "utils", "withr" ], - "Hash": "3bcef49cfb33dcc522ab94eabd5d3714" + "Hash": "a69f815bcba8a055de0b08339b943f9e" }, "rhdf5": { "Package": "rhdf5", @@ -3630,14 +3700,14 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb" + "Hash": "50a6dbdc522936ca35afc5e2082ea91b" }, "rmarkdown": { "Package": "rmarkdown", @@ -3665,13 +3735,13 @@ }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.3", + "Version": "2.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1de7ab598047a87bba48434ba35d497d" + "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" }, "rstudioapi": { "Package": "rstudioapi", @@ -3850,7 +3920,7 @@ }, "sctransform": { "Package": "sctransform", - "Version": "0.4.0", + "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3870,12 +3940,13 @@ "reshape2", "rlang" ], - "Hash": "d55ea018c4cf7ee12c3188c574857755" + "Hash": "0242402f321be0246fb67cf8c63b3572" }, "scuttle": { "Package": "scuttle", - "Version": "1.10.2", + "Version": "1.10.3", "Source": "Bioconductor", + "Repository": "CRAN", "Requirements": [ "BiocGenerics", "BiocParallel", @@ -3892,7 +3963,7 @@ "stats", "utils" ], - "Hash": "c81a27288455b3d22465df1e9cfc9dc0" + "Hash": "5cd19f69bdeb9bae05ab947354ef599a" }, "selectr": { "Package": "selectr", @@ -3935,7 +4006,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.5", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3965,7 +4036,7 @@ "withr", "xtable" ], - "Hash": "438b99792adbe82a8329ad8697d45afe" + "Hash": "3a1f41807d648a908e3c7f0334bf85e6" }, "sitmo": { "Package": "sitmo", @@ -4001,7 +4072,7 @@ }, "sp": { "Package": "sp", - "Version": "2.0-0", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4014,7 +4085,21 @@ "stats", "utils" ], - "Hash": "2551981e6f85d59c81652bf654d6c3ca" + "Hash": "e9090fe4ff468d366aa6a76a9b3ec078" + }, + "spam": { + "Package": "spam", + "Version": "2.10-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "Rcpp", + "dotCall64", + "grid", + "methods" + ], + "Hash": "ffe1f9e95a4375530747b268f82b5086" }, "sparseMatrixStats": { "Package": "sparseMatrixStats", @@ -4031,7 +4116,7 @@ }, "spatstat.data": { "Package": "spatstat.data", - "Version": "3.0-1", + "Version": "3.0-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4039,11 +4124,11 @@ "R", "spatstat.utils" ], - "Hash": "8a96bb2ac0b8e9a92823e0850ae73610" + "Hash": "d84347012166eaea5303b050a3504eb3" }, "spatstat.explore": { "Package": "spatstat.explore", - "Version": "3.2-3", + "Version": "3.2-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4063,11 +4148,11 @@ "stats", "utils" ], - "Hash": "9651f99d8fadfbbda2cd9facca940d29" + "Hash": "81ecb92d6bf49ad7090951e3fe16bd8a" }, "spatstat.geom": { "Package": "spatstat.geom", - "Version": "3.2-5", + "Version": "3.2-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4082,11 +4167,11 @@ "stats", "utils" ], - "Hash": "83fbece32a797f0965ad4953aaac7533" + "Hash": "198af920edce4a6757c2a38217bd0c88" }, "spatstat.random": { "Package": "spatstat.random", - "Version": "3.1-6", + "Version": "3.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4099,11 +4184,11 @@ "stats", "utils" ], - "Hash": "cf3a811e9a8ce9feff6c5b89209ed520" + "Hash": "acc1799b6e8a63068ef4f8108a158538" }, "spatstat.sparse": { "Package": "spatstat.sparse", - "Version": "3.0-2", + "Version": "3.0-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4116,11 +4201,11 @@ "tensor", "utils" ], - "Hash": "82a7d5a77f165b08dae877ef98dc6fcc" + "Hash": "1daaecefd754bb259a5ad5ce95a2cdcc" }, "spatstat.utils": { "Package": "spatstat.utils", - "Version": "3.0-3", + "Version": "3.0-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4131,7 +4216,7 @@ "stats", "utils" ], - "Hash": "8f9764a85e3ca99604625f7ab6012418" + "Hash": "81d929f43f8532c1f8180a105449d414" }, "statmod": { "Package": "statmod", @@ -4147,7 +4232,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4156,11 +4241,11 @@ "tools", "utils" ], - "Hash": "ca8bd84263c77310739d2cf64d84d7c9" + "Hash": "12bf57fdcb9b7068bea39b32f87ecac9" }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4173,7 +4258,7 @@ "stringi", "vctrs" ], - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" + "Hash": "960e2ae9e09656611e0b8214ad543207" }, "survival": { "Package": "survival", @@ -4207,7 +4292,7 @@ }, "svglite": { "Package": "svglite", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4215,7 +4300,7 @@ "cpp11", "systemfonts" ], - "Hash": "29442899581643411facb66f4add846a" + "Hash": "be5318f6b48c136ecd6b8b5de24cc0ae" }, "sys": { "Package": "sys", @@ -4226,14 +4311,14 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "90b28393209827327de889f49935140a" + "Hash": "15b594369e70b975ba9f064295983499" }, "tensor": { "Package": "tensor", @@ -4244,7 +4329,7 @@ }, "testthat": { "Package": "testthat", - "Version": "3.1.10", + "Version": "3.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4270,11 +4355,11 @@ "waldo", "withr" ], - "Hash": "6f403dc49295610a3a67ea1a9ca64346" + "Hash": "877508719fcb8c9525eccdadf07a5102" }, "textshaping": { "Package": "textshaping", - "Version": "0.3.6", + "Version": "0.3.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4282,7 +4367,7 @@ "cpp11", "systemfonts" ], - "Hash": "1ab6223d3670fac7143202cb6a2d43d5" + "Hash": "997aac9ad649e0ef3b97f96cddd5622b" }, "tibble": { "Package": "tibble", @@ -4395,13 +4480,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.46", + "Version": "0.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "0c41a73214d982f539c56a7773c7afa5" + "Hash": "8f96d229b7311beb32b94cf413b13f84" }, "tweenr": { "Package": "tweenr", @@ -4442,13 +4527,13 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "uuid": { "Package": "uuid", @@ -4479,7 +4564,7 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.6.3", + "Version": "0.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4489,7 +4574,7 @@ "lifecycle", "rlang" ], - "Hash": "d0ef2856b83dc33ea6e255caf6229ee2" + "Hash": "266c1ca411266ba8f365fcc726444b87" }, "vipor": { "Package": "vipor", @@ -4528,7 +4613,7 @@ }, "vroom": { "Package": "vroom", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4550,14 +4635,15 @@ "vctrs", "withr" ], - "Hash": "8318e64ffb3a70e652494017ec455561" + "Hash": "9db52c1656cf19c124f93124ea57f0fd" }, "waldo": { "Package": "waldo", - "Version": "0.5.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "cli", "diffobj", "fansi", @@ -4567,7 +4653,7 @@ "rlang", "tibble" ], - "Hash": "2c993415154cdb94649d99ae138ff5e5" + "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6" }, "webshot": { "Package": "webshot", @@ -4584,7 +4670,7 @@ }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "2.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -4593,18 +4679,18 @@ "graphics", "stats" ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" + "Hash": "4b25e70111b7d644322e9513f403a272" }, "xfun": { "Package": "xfun", - "Version": "0.40", + "Version": "0.41", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "stats", "tools" ], - "Hash": "be07d23211245fc7d4209f54c4e4ffc8" + "Hash": "460a5e0fe46a80ef87424ad216028014" }, "xml2": { "Package": "xml2", diff --git a/docker/requirements.txt b/docker/requirements.txt index 779834e2..86a4b11b 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -1,5 +1,5 @@ absl-py==1.4.0 -aiohttp==3.8.5 +aiohttp==3.9.0 aiosignal==1.3.1 anndata==0.9.1 annotated-types==0.5.0 @@ -85,7 +85,7 @@ ordered-set==4.1.0 packaging==23.1 pandas==2.0.1 patsy==0.5.3 -Pillow==9.5.0 +Pillow==10.1.0 protobuf==4.22.3 psutil==5.9.5 pyasn1==0.5.0 @@ -105,7 +105,7 @@ pytorch-lightning==2.0.7 pytz==2023.3 PyYAML==6.0 readchar==4.0.5 -requests==2.29.0 +requests==2.31.0 requests-oauthlib==1.3.1 rich==13.3.5 rsa==4.9 @@ -139,12 +139,12 @@ traitlets==5.9.0 typing_extensions==4.7.1 tzdata==2023.3 umap-learn==0.5.3 -urllib3==1.26.15 +urllib3==2.1.0 uvicorn==0.23.2 wcwidth==0.2.6 websocket-client==1.6.1 websockets==11.0.3 -Werkzeug==2.3.1 +Werkzeug==3.0.1 wrapt==1.14.1 xarray==2023.7.0 yarl==1.9.2 diff --git a/renv/activate.R b/renv/activate.R index 2969c732..cb5401f9 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.2" + version <- "1.0.3" attr(version, "sha") <- NULL # the project directory @@ -1034,19 +1034,6 @@ local({ } - - renv_bootstrap_in_rstudio <- function() { - commandArgs()[[1]] == "RStudio" - } - - # Used to work around buglet in RStudio if hook uses readline - renv_bootstrap_flush_console <- function() { - tryCatch({ - tools <- as.environment("tools:rstudio") - tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) - }, error = function(cnd) {}) - } - renv_json_read <- function(file = NULL, text = NULL) { jlerr <- NULL @@ -1185,16 +1172,8 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - if (renv_bootstrap_in_rstudio()) { - # RStudio only updates console once .Rprofile is finished, so - # instead run code on sessionInit - setHook("rstudio.sessionInit", function(...) { - renv_bootstrap_exec(project, libpath, version) - renv_bootstrap_flush_console() - }) - } else { - renv_bootstrap_exec(project, libpath, version) - } + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) invisible() From 6fa40245a5c36be4a0a23ded28e94e2412b88280 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 22 Nov 2023 15:25:55 -0500 Subject: [PATCH 2/2] Update base R version --- .github/workflows/R-CMD-check-renv.yaml | 2 +- .pre-commit-config.yaml | 1 + docker/Dockerfile | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check-renv.yaml b/.github/workflows/R-CMD-check-renv.yaml index fd1673b6..2a66df21 100644 --- a/.github/workflows/R-CMD-check-renv.yaml +++ b/.github/workflows/R-CMD-check-renv.yaml @@ -26,7 +26,7 @@ jobs: - name: Set up R uses: r-lib/actions/setup-r@v2 with: - r-version: "4.3.1" + r-version: "4.3.2" use-public-rspm: true - name: Set up Pandoc diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 280f85c3..ff20b3e6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -37,6 +37,7 @@ repos: (.*/|)renv/settings\.dcf| (.*/|)renv\.lock| (.*/|)requirements\.txt| + (.*/|)Dockerfile| (.*/|)WORDLIST| \.github/workflows/.*| data/.*| diff --git a/docker/Dockerfile b/docker/Dockerfile index d014c0a2..2307e994 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/r-ver:4.3.1 +FROM rocker/r-ver:4.3.2 LABEL maintainer="ccdl@alexslemonade.org" LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools