From 9f02c0f5f9e93c2cba15a7a273890341354868b9 Mon Sep 17 00:00:00 2001 From: stefanocoretta Date: Sun, 4 Sep 2022 11:03:33 +0100 Subject: [PATCH] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20-=20update=20r=20packages?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- renv.lock | 463 ++++++++++++++++++++++++++-------------------- renv/activate.R | 98 +++++++--- renv/settings.dcf | 2 + 3 files changed, 332 insertions(+), 231 deletions(-) diff --git a/renv.lock b/renv.lock index 67df96c..4dbf13c 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.2", + "Version": "4.2.1", "Repositories": [ { "Name": "CRAN", @@ -9,23 +9,23 @@ ] }, "Bioconductor": { - "Version": "3.14" + "Version": "3.15" }, "Packages": { "BiocManager": { "Package": "BiocManager", - "Version": "1.30.16", + "Version": "1.30.18", "Source": "Repository", "Repository": "CRAN", - "Hash": "2fdca0877debdd4668190832cdee4c31", + "Hash": "b1a93bed5debda5775636086fdca017b", "Requirements": [] }, "DBI": { "Package": "DBI", - "Version": "1.1.2", + "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "dcd1743af4336156873e3ce3c950b8b9", + "Hash": "b2866e62bab9378c3cc9476a1954226b", "Requirements": [] }, "KernSmooth": { @@ -38,28 +38,28 @@ }, "MASS": { "Package": "MASS", - "Version": "7.3-55", + "Version": "7.3-58.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c5232ffb549f6d7a04a152c34ca1353d", + "Hash": "762e1804143a332333c054759f89a706", "Requirements": [] }, "Matrix": { "Package": "Matrix", - "Version": "1.4-0", + "Version": "1.4-1", "Source": "Repository", "Repository": "CRAN", - "Hash": "130c0caba175739d98f2963c6a407cf6", + "Hash": "699c47c606293bdfbc9fd78a93c9c8fe", "Requirements": [ "lattice" ] }, "R.cache": { "Package": "R.cache", - "Version": "0.15.0", + "Version": "0.16.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", + "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", "Requirements": [ "R.methodsS3", "R.oo", @@ -69,28 +69,28 @@ }, "R.methodsS3": { "Package": "R.methodsS3", - "Version": "1.8.1", + "Version": "1.8.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "4bf6453323755202d5909697b6f7c109", + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", "Requirements": [] }, "R.oo": { "Package": "R.oo", - "Version": "1.24.0", + "Version": "1.25.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "5709328352717e2f0a9c012be8a97554", + "Hash": "a0900a114f4f0194cf4aa8cd4a700681", "Requirements": [ "R.methodsS3" ] }, "R.utils": { "Package": "R.utils", - "Version": "2.11.0", + "Version": "2.12.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "a7ecb8e60815c7a18648e84cd121b23a", + "Hash": "d31333e10f14027e1cbbc6f266512806", "Requirements": [ "R.methodsS3", "R.oo" @@ -106,18 +106,18 @@ }, "RColorBrewer": { "Package": "RColorBrewer", - "Version": "1.1-2", + "Version": "1.1-3", "Source": "Repository", "Repository": "CRAN", - "Hash": "e031418365a7f7a766181ab5a41a5716", + "Hash": "45f0398006e83a5b10b72a90663d8d8c", "Requirements": [] }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.8", + "Version": "1.0.9", "Source": "Repository", "Repository": "CRAN", - "Hash": "22b546dd7e337f6c0c58a39983a496bc", + "Hash": "e9c08b94391e9f3f97355841229124f2", "Requirements": [] }, "askpass": { @@ -148,10 +148,10 @@ }, "badger": { "Package": "badger", - "Version": "0.1.0", + "Version": "0.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "014f2c614d8456059504955a322b9999", + "Hash": "947d26ca2f684ec7906181770c86b74b", "Requirements": [ "desc", "dlstats", @@ -187,10 +187,10 @@ }, "blob": { "Package": "blob", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "dc5f7a6598bb025d20d66bb758f12879", + "Hash": "10d231579bc9c06ab1c320618808d4ff", "Requirements": [ "rlang", "vctrs" @@ -222,10 +222,10 @@ }, "broom": { "Package": "broom", - "Version": "0.7.12", + "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "bfa8a039d77ae8d5413254e572c8abea", + "Hash": "c90ff735b7812b60f067a3f7a3b4de63", "Requirements": [ "backports", "dplyr", @@ -242,14 +242,16 @@ }, "bslib": { "Package": "bslib", - "Version": "0.3.1", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "56ae7e1987b340186a8a5a157c2ec358", + "Hash": "be5ee090716ce1671be6cd5d7c34d091", "Requirements": [ + "cachem", "htmltools", "jquerylib", "jsonlite", + "memoise", "rlang", "sass" ] @@ -267,10 +269,10 @@ }, "callr": { "Package": "callr", - "Version": "3.7.0", + "Version": "3.7.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "461aa75a11ce2400245190ef5d3995df", + "Hash": "358689cac9fe93b1bb3a19088d2dbed8", "Requirements": [ "R6", "processx" @@ -299,28 +301,28 @@ }, "cli": { "Package": "cli", - "Version": "3.1.1", + "Version": "3.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "da5160e769a652e3ec7111d63883f9bc", + "Hash": "23abf173c2b783dcc43379ab9bba00ee", "Requirements": [ "glue" ] }, "clipr": { "Package": "clipr", - "Version": "0.7.1", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, "cluster": { "Package": "cluster", - "Version": "2.1.2", + "Version": "2.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "ce49bfe5bc0b3ecd43a01fe1b01c2243", + "Hash": "5edbbabab6ce0bf7900a74fd4358628e", "Requirements": [] }, "codetools": { @@ -341,18 +343,18 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.0-2", + "Version": "2.0-3", "Source": "Repository", "Repository": "CRAN", - "Hash": "6baccb763ee83c0bd313460fdb8b8a84", + "Hash": "bb4341986bc8b914f0f0acf2e4a3f2f7", "Requirements": [] }, "commonmark": { "Package": "commonmark", - "Version": "1.7", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "0f22be39ec1d141fd03683c06f3a6e67", + "Hash": "2ba81b120c1655ab696c935ef33ea716", "Requirements": [] }, "cpp11": { @@ -365,10 +367,10 @@ }, "crayon": { "Package": "crayon", - "Version": "1.4.2", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "0a6a65d92bd45b47b94b84244b528d17", + "Hash": "8dc45fd8a1ee067a92b85ef274e66d6a", "Requirements": [] }, "credentials": { @@ -417,20 +419,21 @@ }, "dbplyr": { "Package": "dbplyr", - "Version": "2.1.1", + "Version": "2.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "1f37fa4ab2f5f7eded42f78b9a887182", + "Hash": "f6c7eb9617e4d2a86bb7182fff99c805", "Requirements": [ "DBI", "R6", "assertthat", "blob", + "cli", "dplyr", - "ellipsis", "glue", "lifecycle", "magrittr", + "pillar", "purrr", "rlang", "tibble", @@ -441,41 +444,42 @@ }, "desc": { "Package": "desc", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "28763d08fadd0b733e3cee9dab4e12fe", + "Hash": "eebd27ee58fcc58714eedb7aa07d8ad1", "Requirements": [ "R6", - "crayon", + "cli", "rprojroot" ] }, "devtools": { "Package": "devtools", - "Version": "2.4.3", + "Version": "2.4.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5", + "Hash": "d6ad91ae6533b84d227bb0b5262c111f", "Requirements": [ - "callr", "cli", "desc", "ellipsis", "fs", - "httr", "lifecycle", "memoise", + "miniUI", "pkgbuild", + "pkgdown", "pkgload", + "profvis", "rcmdcheck", "remotes", "rlang", "roxygen2", - "rstudioapi", "rversions", "sessioninfo", "testthat", + "urlchecker", "usethis", "withr" ] @@ -500,10 +504,10 @@ }, "dlstats": { "Package": "dlstats", - "Version": "0.1.4", + "Version": "0.1.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "7fa98978434fd311584e3aef5b7b3abe", + "Hash": "73932ec955228bb5d6b1c06dff3b2481", "Requirements": [ "RColorBrewer", "ggplot2", @@ -514,10 +518,10 @@ }, "downlit": { "Package": "downlit", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "ba63dc9ab5a31f3209892437e40c5f60", + "Hash": "79bf3f66590752ffbba20f8d2da94c7c", "Requirements": [ "brio", "desc", @@ -527,15 +531,16 @@ "memoise", "rlang", "vctrs", + "withr", "yaml" ] }, "dplyr": { "Package": "dplyr", - "Version": "1.0.8", + "Version": "1.0.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "ef47665e64228a17609d6df877bf86f2", + "Hash": "539412282059f7f0c07295723d23f987", "Requirements": [ "R6", "generics", @@ -551,10 +556,10 @@ }, "dtplyr": { "Package": "dtplyr", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "f5d195cd5fcc0a77499d9da698ef2ea3", + "Hash": "c5f8828a0b459a703db190b001ad4818", "Requirements": [ "crayon", "data.table", @@ -580,26 +585,26 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.14", + "Version": "0.16", "Source": "Repository", "Repository": "CRAN", - "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", + "Hash": "9a3d3c345f8a5648abe61608aaa29518", "Requirements": [] }, "fansi": { "Package": "fansi", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "f28149c2d7a1342a834b314e95e67260", + "Hash": "83a8afdbe71839506baa9f90eebad7ec", "Requirements": [] }, "farver": { "Package": "farver", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c98eb5133d9cb9e1622b8691487f11bb", + "Hash": "8106d78941f34855c440ddb946b8f7a5", "Requirements": [] }, "fastmap": { @@ -612,10 +617,10 @@ }, "fontawesome": { "Package": "fontawesome", - "Version": "0.2.2", + "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "55624ed409e46c5f358b2c060be87f67", + "Hash": "a36c4a3eade472039a3ec8cb824e6dc4", "Requirements": [ "htmltools", "rlang" @@ -623,15 +628,19 @@ }, "forcats": { "Package": "forcats", - "Version": "0.5.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "81c3244cab67468aac4c60550832655d", + "Hash": "9d95bc88206321cd1bc98480ecfd74bb", "Requirements": [ + "cli", "ellipsis", + "glue", + "lifecycle", "magrittr", "rlang", - "tibble" + "tibble", + "withr" ] }, "foreign": { @@ -670,18 +679,18 @@ }, "generics": { "Package": "generics", - "Version": "0.1.2", + "Version": "0.1.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "177475892cf4a55865868527654a7741", + "Hash": "15e9634c0fcd294799e9b2e929ed1b86", "Requirements": [] }, "gert": { "Package": "gert", - "Version": "1.5.0", + "Version": "1.7.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "8fddce7cbd59467106266a6e93e253b4", + "Hash": "92d17e7b0639cad43d44e75199d4aa64", "Requirements": [ "askpass", "credentials", @@ -693,10 +702,10 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.3.5", + "Version": "3.3.6", "Source": "Repository", "Repository": "CRAN", - "Hash": "d7566c471c7b17e095dd023b9ef155ad", + "Hash": "0fb26d0674c82705c6b701d1a61e02ea", "Requirements": [ "MASS", "digest", @@ -734,10 +743,10 @@ }, "glue": { "Package": "glue", - "Version": "1.6.1", + "Version": "1.6.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "de07842fc27ebf60e1102091c0c85e47", + "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, "googledrive": { @@ -765,10 +774,10 @@ }, "googlesheets4": { "Package": "googlesheets4", - "Version": "1.0.0", + "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "9a6564184dc4a81daea4f1d7ce357c6a", + "Hash": "3b449d5292327880fc6cb61d0b2e9063", "Requirements": [ "cellranger", "cli", @@ -788,22 +797,24 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.0", + "Version": "0.3.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "ac5c6baf7822ce8732b343f14c072c4d", + "Hash": "36b4265fb818f6a342bed217549cd896", "Requirements": [] }, "haven": { "Package": "haven", - "Version": "2.4.3", + "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "10bec8a8264f3eb59531e8c4c0303f96", + "Hash": "5b45a553fca2217a07b6f9c843304c44", "Requirements": [ + "cli", "cpp11", "forcats", "hms", + "lifecycle", "readr", "rlang", "tibble", @@ -823,10 +834,10 @@ }, "hms": { "Package": "hms", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca", + "Hash": "41100392191e1244b887878b533eea91", "Requirements": [ "ellipsis", "lifecycle", @@ -837,10 +848,10 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "526c484233f42522278ab06fb185cb26", + "Hash": "6496090a9e00f8354b811d1a2d47b566", "Requirements": [ "base64enc", "digest", @@ -848,6 +859,18 @@ "rlang" ] }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.5.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", + "Requirements": [ + "htmltools", + "jsonlite", + "yaml" + ] + }, "httpuv": { "Package": "httpuv", "Version": "1.6.5", @@ -863,10 +886,10 @@ }, "httr": { "Package": "httr", - "Version": "1.4.2", + "Version": "1.4.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "a525aba14184fec243f9eaec62fbed43", + "Hash": "57557fac46471f0dbbf44705cc6a5c8c", "Requirements": [ "R6", "curl", @@ -914,18 +937,18 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.7.3", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "68c37fd8f863c6273dcd24928c17d6e1", + "Hash": "d07e729b27b372429d42d24d503613a0", "Requirements": [] }, "knitr": { "Package": "knitr", - "Version": "1.37", + "Version": "1.40", "Source": "Repository", "Repository": "CRAN", - "Hash": "a4ec675eb332a33fe7b7fe26f70e1f98", + "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", "highr", @@ -944,10 +967,10 @@ }, "languageserver": { "Package": "languageserver", - "Version": "0.3.12", + "Version": "0.3.13", "Source": "Repository", "Repository": "CRAN", - "Hash": "f62ed8b09fd56cd70291bd077bc52c4b", + "Hash": "ee396ad16694fbb3fca42646c6349dd3", "Requirements": [ "R6", "callr", @@ -1002,21 +1025,20 @@ }, "lintr": { "Package": "lintr", - "Version": "2.0.1", + "Version": "3.0.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "023cecbdc0a32f86ad3cb1734c018d2e", + "Hash": "1214604176fb93fdcac030fc5d2177d9", "Requirements": [ + "backports", "codetools", "crayon", "cyclocomp", "digest", - "httr", + "glue", "jsonlite", "knitr", "rex", - "rstudioapi", - "testthat", "xml2", "xmlparsedata" ] @@ -1034,10 +1056,10 @@ }, "magrittr": { "Package": "magrittr", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "cdc87ecd81934679d1557633d8e1fe51", + "Hash": "7ce2733a9826b3aeb1775d56fd305472", "Requirements": [] }, "markdown": { @@ -1064,10 +1086,10 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.8-38", + "Version": "1.8-40", "Source": "Repository", "Repository": "CRAN", - "Hash": "be3c61ffbb1e3d3b3df214d192ac5444", + "Hash": "c6b2fdb18cf68ab613bd564363e1ba0d", "Requirements": [ "Matrix", "nlme" @@ -1081,12 +1103,23 @@ "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, + "miniUI": { + "Package": "miniUI", + "Version": "0.1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fec5f52652d60615fdb3957b3d74324a", + "Requirements": [ + "htmltools", + "shiny" + ] + }, "modelr": { "Package": "modelr", - "Version": "0.1.8", + "Version": "0.1.9", "Source": "Repository", "Repository": "CRAN", - "Hash": "9fd59716311ee82cba83dc2826fc5577", + "Hash": "ce70fef14a09fd1cab1f3792a0e210c1", "Requirements": [ "broom", "magrittr", @@ -1110,10 +1143,10 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-155", + "Version": "3.1-159", "Source": "Repository", "Repository": "CRAN", - "Hash": "74ad940dccc9e977189a5afe5fcdb7ba", + "Hash": "4a0b3a68f846cb999ff0e8e519524fbb", "Requirements": [ "lattice" ] @@ -1128,24 +1161,22 @@ }, "openssl": { "Package": "openssl", - "Version": "1.4.6", + "Version": "2.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "69fdf291af288f32fd4cd93315084ea8", + "Hash": "6d3bef2e305f55c705c674653c7d7d3d", "Requirements": [ "askpass" ] }, "pillar": { "Package": "pillar", - "Version": "1.7.0", + "Version": "1.8.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e", + "Hash": "f2316df30902c81729ae9de95ad5a608", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", "glue", "lifecycle", @@ -1181,14 +1212,14 @@ }, "pkgdown": { "Package": "pkgdown", - "Version": "2.0.2", + "Version": "2.0.6", "Source": "Repository", "Repository": "CRAN", - "Hash": "1ef66f10b752bb5f17e33fe9fa861005", + "Hash": "f958d0b2a5dabc5ffd414f062b1ffbe7", "Requirements": [ "bslib", "callr", - "crayon", + "cli", "desc", "digest", "downlit", @@ -1210,17 +1241,18 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.2.4", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "7533cd805940821bf23eaf3c8d4c1735", + "Hash": "4b20f937a363c78a5730265c1925f54a", "Requirements": [ "cli", "crayon", "desc", + "fs", + "glue", "rlang", "rprojroot", - "rstudioapi", "withr" ] }, @@ -1242,15 +1274,26 @@ }, "processx": { "Package": "processx", - "Version": "3.5.2", + "Version": "3.7.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "0cbca2bc4d16525d009c4dbba156b37c", + "Hash": "f91df0f5f31ffdf88bc0b624f5ebab0f", "Requirements": [ "R6", "ps" ] }, + "profvis": { + "Package": "profvis", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", + "Requirements": [ + "htmlwidgets", + "stringr" + ] + }, "progress": { "Package": "progress", "Version": "1.2.2", @@ -1280,10 +1323,10 @@ }, "ps": { "Package": "ps", - "Version": "1.6.0", + "Version": "1.7.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "32620e2001c1dce1af49c49dccbb9420", + "Hash": "8b93531308c01ad0e56d9eadcc0c4fcd", "Requirements": [] }, "purrr": { @@ -1299,10 +1342,10 @@ }, "ragg": { "Package": "ragg", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "4577b3859de34ffb2938d9a878dcf384", + "Hash": "14932bb6f2739c771ca4ceaba6b4248e", "Requirements": [ "systemfonts", "textshaping" @@ -1359,13 +1402,13 @@ }, "readxl": { "Package": "readxl", - "Version": "1.3.1", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "63537c483c2dbec8d9e3183b3735254a", + "Hash": "5c1fbc365ac0a3fe7728ac79108b8e64", "Requirements": [ - "Rcpp", "cellranger", + "cpp11", "progress", "tibble" ] @@ -1398,18 +1441,18 @@ }, "renv": { "Package": "renv", - "Version": "0.15.2", + "Version": "0.15.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "206c4ef8b7ad6fb1060d69aa7b9dfe69", + "Hash": "6a38294e7d12f5d8e656b08c5bd8ae34", "Requirements": [] }, "reprex": { "Package": "reprex", - "Version": "2.0.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "911d101becedc0fde495bd910984bdc8", + "Hash": "d66fe009d4c20b7ab1927eb405db9ee2", "Requirements": [ "callr", "cli", @@ -1417,6 +1460,7 @@ "fs", "glue", "knitr", + "lifecycle", "rlang", "rmarkdown", "rstudioapi", @@ -1435,19 +1479,20 @@ }, "rlang": { "Package": "rlang", - "Version": "1.0.1", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "3bf0219f19d9f5b3c682acbb3546a151", + "Hash": "971c3d698fc06dabdac6bc4bcda72dc4", "Requirements": [] }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.11", + "Version": "2.16", "Source": "Repository", "Repository": "CRAN", - "Hash": "320017b52d05a943981272b295750388", + "Hash": "0f3eaa1547e2c6880d4de1c043ac6826", "Requirements": [ + "bslib", "evaluate", "htmltools", "jquerylib", @@ -1461,13 +1506,14 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.1.2", + "Version": "7.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "eb9849556c4250305106e82edae35b72", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", + "cli", "commonmark", "cpp11", "desc", @@ -1478,6 +1524,7 @@ "rlang", "stringi", "stringr", + "withr", "xml2" ] }, @@ -1491,18 +1538,18 @@ }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", + "Hash": "1de7ab598047a87bba48434ba35d497d", "Requirements": [] }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.13", + "Version": "0.14", "Source": "Repository", "Repository": "CRAN", - "Hash": "06c85365a03fdaf699966cc1d3cf53ea", + "Hash": "690bd2acc42a9166ce34845884459320", "Requirements": [] }, "rvcheck": { @@ -1518,10 +1565,10 @@ }, "rversions": { "Package": "rversions", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "f88fab00907b312f8b23ec13e2d437cb", + "Hash": "a9881dfed103e83f9de151dc17002cd1", "Requirements": [ "curl", "xml2" @@ -1529,26 +1576,29 @@ }, "rvest": { "Package": "rvest", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "bb099886deffecd6f9b298b7d4492943", + "Hash": "a4a5ac819a467808c60e36e92ddf195e", "Requirements": [ + "cli", + "glue", "httr", "lifecycle", "magrittr", "rlang", "selectr", "tibble", + "withr", "xml2" ] }, "sass": { "Package": "sass", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "50cf822feb64bb3977bda0b7091be623", + "Hash": "1b191143d7d3444d504277843f3a95fe", "Requirements": [ "R6", "fs", @@ -1559,10 +1609,10 @@ }, "scales": { "Package": "scales", - "Version": "1.1.1", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "6f76f71042411426ec8df6c54f34e6dd", + "Hash": "906cb23d2f1c5680b8ce439b44c6fa63", "Requirements": [ "R6", "RColorBrewer", @@ -1570,6 +1620,7 @@ "labeling", "lifecycle", "munsell", + "rlang", "viridisLite" ] }, @@ -1596,10 +1647,10 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.1", + "Version": "1.7.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "00344c227c7bd0ab5d78052c5d736c44", + "Hash": "4f7970a3edb0a153ac6b376785a1944a", "Requirements": [ "R6", "bslib", @@ -1641,18 +1692,18 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.6", + "Version": "1.7.8", "Source": "Repository", "Repository": "CRAN", - "Hash": "bba431031d30789535745a9627ac9271", + "Hash": "a68b980681bcbc84c7a67003fa796bfb", "Requirements": [] }, "stringr": { "Package": "stringr", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "0759e6b6c0957edb1311028a49a35e76", + "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5", "Requirements": [ "glue", "magrittr", @@ -1661,31 +1712,28 @@ }, "styler": { "Package": "styler", - "Version": "1.6.2", + "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "d9e85c794c5a723aabed32a49926186a", + "Hash": "6cc6b1eb8f318b15fae4b81fe0a0d82e", "Requirements": [ "R.cache", - "backports", "cli", - "glue", "magrittr", "purrr", "rematch2", "rlang", "rprojroot", "tibble", - "withr", - "xfun" + "withr" ] }, "survival": { "Package": "survival", - "Version": "3.2-13", + "Version": "3.4-0", "Source": "Repository", "Repository": "CRAN", - "Hash": "6f0a0fadc63bc6570fe172770f15bbc4", + "Hash": "04411ae66ab4659230c067c32966fc20", "Requirements": [ "Matrix" ] @@ -1710,10 +1758,10 @@ }, "testthat": { "Package": "testthat", - "Version": "3.1.2", + "Version": "3.1.4", "Source": "Repository", "Repository": "CRAN", - "Hash": "32454e5780e8dbe31e4b61b13d8918fe", + "Hash": "f76c2a02d0fdc24aa7a47ea34261a6e3", "Requirements": [ "R6", "brio", @@ -1749,12 +1797,11 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.6", + "Version": "3.1.8", "Source": "Repository", "Repository": "CRAN", - "Hash": "8a8f02d1934dfd6431c671361510dd0b", + "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ - "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1786,10 +1833,10 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.1", + "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "7243004a708d06d4716717fa1ff5b2fe", + "Hash": "17f6da8cfd7002760a859915ce7eef8f", "Requirements": [ "ellipsis", "glue", @@ -1800,10 +1847,10 @@ }, "tidyverse": { "Package": "tidyverse", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "fc4c72b6ae9bb283416bd59a3303bbab", + "Hash": "972389aea7fa1a34739054a810d0c6f6", "Requirements": [ "broom", "cli", @@ -1838,30 +1885,42 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.36", + "Version": "0.41", "Source": "Repository", "Repository": "CRAN", - "Hash": "130fe4c61e55b271a2655b3a284a205f", + "Hash": "6edfe5df6431a724b4254c0591e34ab3", "Requirements": [ "xfun" ] }, "tzdb": { "Package": "tzdb", - "Version": "0.2.0", + "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "5e069fb033daf2317bd628d3100b75c5", + "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e", "Requirements": [ "cpp11" ] }, + "urlchecker": { + "Package": "urlchecker", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "409328b8e1253c8d729a7836fe7f7a16", + "Requirements": [ + "cli", + "curl", + "xml2" + ] + }, "usethis": { "Package": "usethis", - "Version": "2.1.5", + "Version": "2.1.6", "Source": "Repository", "Repository": "CRAN", - "Hash": "c499f488e6dd7718accffaee5bc5a79b", + "Hash": "a67a22c201832b12c036cc059f1d137d", "Requirements": [ "cli", "clipr", @@ -1894,30 +1953,30 @@ }, "uuid": { "Package": "uuid", - "Version": "1.0-3", + "Version": "1.1-0", "Source": "Repository", "Repository": "CRAN", - "Hash": "2097822ba5e4440b81a0c7525d0315ce", + "Hash": "f1cb46c157d080b729159d407be83496", "Requirements": [] }, "vctrs": { "Package": "vctrs", - "Version": "0.3.8", + "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "ecf749a1b39ea72bd9b51b76292261f1", + "Hash": "8b54f22e2a58c4f275479c92ce041a57", "Requirements": [ - "ellipsis", + "cli", "glue", "rlang" ] }, "viridisLite": { "Package": "viridisLite", - "Version": "0.4.0", + "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "55e157e2aa88161bdb0754218470d204", + "Hash": "62f4b5da3e08d8e5bcba6cac15603f70", "Requirements": [] }, "vroom": { @@ -1945,10 +2004,10 @@ }, "waldo": { "Package": "waldo", - "Version": "0.3.1", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "ad8cfff5694ac5b3c354f8f2044bd976", + "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", "diffobj", @@ -1969,18 +2028,18 @@ }, "withr": { "Package": "withr", - "Version": "2.4.3", + "Version": "2.5.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "a376b424c4817cda4920bbbeb3364e85", + "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, "xfun": { "Package": "xfun", - "Version": "0.29", + "Version": "0.32", "Source": "Repository", "Repository": "CRAN", - "Hash": "e2e5fb1a74fbb68b27d6efc5372635dc", + "Hash": "0498af3034691dde715dcd86198efe75", "Requirements": [] }, "xml2": { @@ -2019,18 +2078,18 @@ }, "yaml": { "Package": "yaml", - "Version": "2.2.2", + "Version": "2.3.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "4597f73aad7d32c2913ec33a345f900b", + "Hash": "458bb38374d73bf83b1bb85e353da200", "Requirements": [] }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.0.4", + "Version": "0.0.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "922e11dcf40bb5dfcf3fe5e714d0dc35", + "Hash": "5727ef3682ea54af05114ef993b99812", "Requirements": [] }, "zip": { diff --git a/renv/activate.R b/renv/activate.R index 33833ee..72c0818 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "0.15.2" + version <- "0.15.5" # the project directory project <- getwd() @@ -54,20 +54,10 @@ local({ # mask 'utils' packages, will come first on the search path library(utils, lib.loc = .Library) - # check to see if renv has already been loaded - if ("renv" %in% loadedNamespaces()) { - - # if renv has already been loaded, and it's the requested version of renv, - # nothing to do - spec <- .getNamespaceInfo(.getNamespace("renv"), "spec") - if (identical(spec[["version"]], version)) - return(invisible(TRUE)) - - # otherwise, unload and attempt to load the correct version of renv + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) unloadNamespace("renv") - } - # load bootstrap tools `%||%` <- function(x, y) { if (is.environment(x) || length(x)) x else y @@ -158,16 +148,20 @@ local({ nv <- numeric_version(version) components <- unclass(nv)[[1]] - methods <- if (length(components) == 4L) { - list( + # if this appears to be a development version of 'renv', we'll + # try to restore from github + dev <- length(components) == 4L + + # begin collecting different methods for finding renv + methods <- c( + renv_bootstrap_download_tarball, + if (dev) renv_bootstrap_download_github - ) - } else { - list( + else c( renv_bootstrap_download_cran_latest, renv_bootstrap_download_cran_archive ) - } + ) for (method in methods) { path <- tryCatch(method(version), error = identity) @@ -304,6 +298,42 @@ local({ } + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + info <- file.info(tarball, extra_cols = FALSE) + if (identical(info$isdir, TRUE)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + fmt <- "* Bootstrapping with tarball at path '%s'." + msg <- sprintf(fmt, tarball) + message(msg) + + tarball + + } + renv_bootstrap_download_github <- function(version) { enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") @@ -357,7 +387,13 @@ local({ bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" r <- file.path(bin, exe) - args <- c("--vanilla", "CMD", "INSTALL", "--no-multiarch", "-l", shQuote(library), shQuote(tarball)) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + output <- system2(r, args, stdout = TRUE, stderr = TRUE) message("Done!") @@ -731,12 +767,17 @@ local({ } - renv_bootstrap_user_dir <- function(path) { - dir <- renv_bootstrap_user_dir_impl(path) - chartr("\\", "/", dir) + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) } - renv_bootstrap_user_dir_impl <- function(path) { + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) # use R_user_dir if available tools <- asNamespace("tools") @@ -747,10 +788,8 @@ local({ envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") for (envvar in envvars) { root <- Sys.getenv(envvar, unset = NA) - if (!is.na(root)) { - path <- file.path(root, "R/renv") - return(path) - } + if (!is.na(root)) + return(file.path(root, "R/renv")) } # use platform-specific default fallbacks @@ -763,13 +802,14 @@ local({ } + renv_json_read <- function(file = NULL, text = NULL) { text <- paste(text %||% read(file), collapse = "\n") # find strings in the JSON pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text)[[1]] + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] # if any are found, replace them with placeholders replaced <- text diff --git a/renv/settings.dcf b/renv/settings.dcf index 205616d..d5893b9 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,8 +1,10 @@ +bioconductor.version: 3.15 external.libraries: ignored.packages: package.dependency.fields: Imports, Depends, LinkingTo r.version: snapshot.type: all use.cache: TRUE +vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE vcs.ignore.local: TRUE