From 8720b43e07bcf2143562dd721d65d980f917a333 Mon Sep 17 00:00:00 2001 From: zkamvar Date: Tue, 7 Nov 2023 00:55:22 +0000 Subject: [PATCH] [actions] update 48 packages --- renv/activate.R | 27 +-- renv/profiles/lesson-requirements/renv.lock | 191 +++++++++++--------- 2 files changed, 104 insertions(+), 114 deletions(-) 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() diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 0d8c493b..614d975c 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -210,7 +210,7 @@ }, "DOSE": { "Package": "DOSE", - "Version": "3.26.1", + "Version": "3.26.2", "Source": "Bioconductor", "Requirements": [ "AnnotationDbi", @@ -226,11 +226,11 @@ "stats", "utils" ], - "Hash": "adf53d60be91fa7a3e2687591993d9f7" + "Hash": "d33bf9add091a5f7bb152809af75be9c" }, "DT": { "Package": "DT", - "Version": "0.29", + "Version": "0.30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -243,7 +243,7 @@ "magrittr", "promises" ], - "Hash": "02f42b77a951a5ea7c891ef5c187d774" + "Hash": "dffb4d94a00be1b4a4507e53ab95bd90" }, "DelayedArray": { "Package": "DelayedArray", @@ -316,7 +316,7 @@ }, "GenomeInfoDb": { "Package": "GenomeInfoDb", - "Version": "1.36.2", + "Version": "1.36.4", "Source": "Bioconductor", "Requirements": [ "BiocGenerics", @@ -330,7 +330,7 @@ "stats4", "utils" ], - "Hash": "94cae1161cc7a68e9e28a2a4994beb72" + "Hash": "1c6756527d78e8135d34662d2e1d54ec" }, "GenomeInfoDbData": { "Package": "GenomeInfoDbData", @@ -343,7 +343,7 @@ }, "GenomicRanges": { "Package": "GenomicRanges", - "Version": "1.52.0", + "Version": "1.52.1", "Source": "Bioconductor", "Requirements": [ "BiocGenerics", @@ -357,7 +357,7 @@ "stats4", "utils" ], - "Hash": "dc2970e434666341650a7983435597bf" + "Hash": "c9471497a07953ded9b8889879c079e9" }, "GetoptLong": { "Package": "GetoptLong", @@ -414,7 +414,7 @@ }, "KEGGREST": { "Package": "KEGGREST", - "Version": "1.40.0", + "Version": "1.40.1", "Source": "Bioconductor", "Requirements": [ "Biostrings", @@ -423,7 +423,7 @@ "methods", "png" ], - "Hash": "b5a4bf06281c694bc38412812c70b011" + "Hash": "2988b310648d92e9d5c877d627068b9d" }, "KernSmooth": { "Package": "KernSmooth", @@ -453,7 +453,7 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1", + "Version": "1.6-1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -466,7 +466,7 @@ "stats", "utils" ], - "Hash": "cb6855ac711958ca734b75e631b2035d" + "Hash": "1a00d4828f33a9d690806e98bd17150c" }, "MatrixGenerics": { "Package": "MatrixGenerics", @@ -500,7 +500,7 @@ }, "RCurl": { "Package": "RCurl", - "Version": "1.98-1.12", + "Version": "1.98-1.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -508,11 +508,11 @@ "bitops", "methods" ], - "Hash": "1d6ed2d006d483f31c6d5531f3a39923" + "Hash": "318c7b8d68358b45cbc6115dda23d7db" }, "RSQLite": { "Package": "RSQLite", - "Version": "2.3.1", + "Version": "2.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -526,7 +526,7 @@ "pkgconfig", "plogr" ], - "Hash": "207c90cd5438a1f596da2cd54c606fee" + "Hash": "3de9b130745b42015c060758cf6d9b8d" }, "Rcpp": { "Package": "Rcpp", @@ -541,7 +541,7 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.6.3.0", + "Version": "0.12.6.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -551,32 +551,31 @@ "stats", "utils" ], - "Hash": "4a4fc9c9d0d24ee8708bb17528372f30" + "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" }, "RcppNumerical": { "Package": "RcppNumerical", - "Version": "0.5-0", + "Version": "0.6-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp", "RcppEigen" ], - "Hash": "04d7d475a3be6fc39e2961227e74c477" + "Hash": "a008f094e60e88cef2472ef0e057f90e" }, "S4Arrays": { "Package": "S4Arrays", @@ -597,7 +596,7 @@ }, "S4Vectors": { "Package": "S4Vectors", - "Version": "0.38.1", + "Version": "0.38.2", "Source": "Bioconductor", "Requirements": [ "BiocGenerics", @@ -607,7 +606,7 @@ "stats4", "utils" ], - "Hash": "f0a46e23a2a7d6aa27e945faf7f242c7" + "Hash": "338207894998073e7823706f886a1386" }, "SingleCellExperiment": { "Package": "SingleCellExperiment", @@ -757,7 +756,7 @@ }, "aplot": { "Package": "aplot", - "Version": "0.2.0", + "Version": "0.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -770,7 +769,7 @@ "patchwork", "utils" ], - "Hash": "391be0aec49261b94791f20cb863c0b7" + "Hash": "869a35e6d38fe9936eb578e09091842b" }, "askpass": { "Package": "askpass", @@ -952,7 +951,7 @@ }, "clue": { "Package": "clue", - "Version": "0.3-64", + "Version": "0.3-65", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -962,7 +961,7 @@ "methods", "stats" ], - "Hash": "f013e45eb656a4bb17b39cb24827a51f" + "Hash": "d6b53853800595408a776900bcc0c23f" }, "cluster": { "Package": "cluster", @@ -1118,13 +1117,13 @@ }, "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", @@ -1223,7 +1222,7 @@ }, "enrichplot": { "Package": "enrichplot", - "Version": "1.20.1", + "Version": "1.20.3", "Source": "Bioconductor", "Requirements": [ "DOSE", @@ -1231,6 +1230,7 @@ "R", "RColorBrewer", "aplot", + "ggfun", "ggnewscale", "ggplot2", "ggraph", @@ -1250,22 +1250,22 @@ "utils", "yulab.utils" ], - "Hash": "2c3a0a3515aef213333b77104bcdf22a" + "Hash": "e3706da8c0221f8592e80699c8a62a5d" }, "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": [ @@ -1273,7 +1273,7 @@ "grDevices", "utils" ], - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" + "Hash": "3e8583a60163b4bc1a80016e63b9959e" }, "farver": { "Package": "farver", @@ -1431,17 +1431,18 @@ }, "ggfun": { "Package": "ggfun", - "Version": "0.1.2", + "Version": "0.1.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "cli", "ggplot2", "grid", "rlang", "utils" ], - "Hash": "068a90b74406f3abb0647635a2696880" + "Hash": "4657d320971a330ecffd0e1260f58214" }, "ggnewscale": { "Package": "ggnewscale", @@ -1455,9 +1456,9 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.3", + "Version": "3.4.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "MASS", "R", @@ -1476,7 +1477,7 @@ "vctrs", "withr" ], - "Hash": "85846544c596e71f8f46483ab165da33" + "Hash": "313d31eff2274ecf4c1d3581db7241f9" }, "ggplotify": { "Package": "ggplotify", @@ -1527,7 +1528,7 @@ }, "ggrepel": { "Package": "ggrepel", - "Version": "0.9.3", + "Version": "0.9.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1539,7 +1540,7 @@ "scales", "withr" ], - "Hash": "92edfac53774706b4d6099f3ee6f6306" + "Hash": "e9839af82cc43fda486a638b68b439b2" }, "ggtree": { "Package": "ggtree", @@ -1596,7 +1597,7 @@ }, "graphlayouts": { "Package": "graphlayouts", - "Version": "1.0.0", + "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1605,7 +1606,7 @@ "RcppArmadillo", "igraph" ], - "Hash": "8e6e2044b72071ae7ea601808887423c" + "Hash": "468c98df6feea8aacf159eee906e7ee8" }, "gridExtra": { "Package": "gridExtra", @@ -1717,7 +1718,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.6", + "Version": "0.5.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1730,7 +1731,7 @@ "rlang", "utils" ], - "Hash": "a2326a66919a3311f7fbb1e3bf568283" + "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -1749,9 +1750,9 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.11", + "Version": "1.6.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://carpentries.r-universe.dev", "Requirements": [ "R", "R6", @@ -1760,7 +1761,7 @@ "promises", "utils" ], - "Hash": "838602f54e32c1a0f8cc80708cefcefa" + "Hash": "c992f75861325961c29a188b45e549f7" }, "httr": { "Package": "httr", @@ -1877,7 +1878,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.43", + "Version": "1.45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1889,7 +1890,7 @@ "xfun", "yaml" ], - "Hash": "9775eb076713f627c07ce41d8199d8f6" + "Hash": "1ec462871063897135c1bcbe0fc8f07d" }, "labeling": { "Package": "labeling", @@ -1926,7 +1927,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.21-8", + "Version": "0.22-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1937,7 +1938,7 @@ "stats", "utils" ], - "Hash": "0b8a6d63c8770f02a8b5635f3c431e6b" + "Hash": "7c5e89f04e72d6611c77451f6331a091" }, "lazyeval": { "Package": "lazyeval", @@ -2132,13 +2133,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "273a6bb4a9844c296a459d2176673270" + "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" }, "org.Hs.eg.db": { "Package": "org.Hs.eg.db", @@ -2216,14 +2217,14 @@ }, "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", @@ -2237,13 +2238,13 @@ }, "polyclip": { "Package": "polyclip", - "Version": "1.10-4", + "Version": "1.10-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "66bbfa06f78108ee967220643596c91e" + "Hash": "436542aadb70675e361cf359285af7c7" }, "preprocessCore": { "Package": "preprocessCore", @@ -2310,13 +2311,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "4b22ac016fe54028b88d0c68badbd061" + "Hash": "41b847654f567341725473431dd0d5ab" }, "reshape2": { "Package": "reshape2", @@ -2333,7 +2334,7 @@ }, "rintrojs": { "Package": "rintrojs", - "Version": "0.3.2", + "Version": "0.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2341,7 +2342,7 @@ "jsonlite", "shiny" ], - "Hash": "c7542d0e29c0cf0a04eb9dc898be5a15" + "Hash": "22b1346426a5dbed5725ace115be32ca" }, "rjson": { "Package": "rjson", @@ -2355,18 +2356,18 @@ }, "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", - "Version": "2.24", + "Version": "2.25", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2386,7 +2387,7 @@ "xfun", "yaml" ], - "Hash": "3854c37590717c08c32ec8542a2e0a35" + "Hash": "d65e35823c817f09f4de424fcdfa812a" }, "sass": { "Package": "sass", @@ -2466,7 +2467,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.5", + "Version": "1.7.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2496,7 +2497,7 @@ "withr", "xtable" ], - "Hash": "438b99792adbe82a8329ad8697d45afe" + "Hash": "5ec01cc255f2138fc2f0dc74d2b1a1a1" }, "shinyAce": { "Package": "shinyAce", @@ -2617,14 +2618,14 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "https://carpentries.r-universe.dev", "Requirements": [ "R", "cpp11" ], - "Hash": "90b28393209827327de889f49935140a" + "Hash": "15b594369e70b975ba9f064295983499" }, "tibble": { "Package": "tibble", @@ -2730,32 +2731,38 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.46", + "Version": "0.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "0c41a73214d982f539c56a7773c7afa5" + "Hash": "8f96d229b7311beb32b94cf413b13f84" }, "treeio": { "Package": "treeio", - "Version": "1.24.3", - "Source": "Bioconductor", + "Version": "1.27.0", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "GuangchuangYu", + "RemoteRepo": "treeio", + "RemoteRef": "devel", + "RemoteSha": "a8b64d4a3ac47406684f573f6e94080ff1e95b2d", "Requirements": [ "R", "ape", - "cli", "dplyr", "jsonlite", "magrittr", "methods", "rlang", + "stats", "tibble", "tidytree", "utils" ], - "Hash": "c8c8efbcec2f1512d6079af62b0f112b" + "Hash": "cdce4cde2d2f25f0de840b9b344c2303" }, "tweenr": { "Package": "tweenr", @@ -2774,17 +2781,17 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "vctrs": { "Package": "vctrs", - "Version": "0.6.3", + "Version": "0.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2794,7 +2801,7 @@ "lifecycle", "rlang" ], - "Hash": "d0ef2856b83dc33ea6e255caf6229ee2" + "Hash": "266c1ca411266ba8f365fcc726444b87" }, "vipor": { "Package": "vipor", @@ -2848,7 +2855,7 @@ }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "2.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2857,18 +2864,18 @@ "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" }, "xtable": { "Package": "xtable", @@ -2891,16 +2898,20 @@ }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.0.9", + "Version": "0.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "cli", + "digest", + "fs", "memoise", "rlang", "stats", + "tools", "utils" ], - "Hash": "2435cde407c69abd057343ab6ce386d0" + "Hash": "792b3c5bc98f04a7d49cbd8c55fe0770" }, "zlibbioc": { "Package": "zlibbioc",