diff --git a/R/edcs.R b/R/edcs.R index 36895d7..876a45a 100644 --- a/R/edcs.R +++ b/R/edcs.R @@ -14,7 +14,8 @@ edcs_information <- function() { pubchem_cid = "", ctd_id = "", exposome_explorer_id = "", - parental_compound = "" + parental_compound = "", + molar_mass = "" # g/mol, also known as molecular weight ) .names <- names(template) @@ -27,7 +28,8 @@ edcs_information <- function() { pubchem_cid = "9274", ctd_id = "C000654497", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 186.2 ), dep = list( full_name = "diethyl phosphate", @@ -37,7 +39,8 @@ edcs_information <- function() { pubchem_cid = "654", ctd_id = "C034789", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 154.10 ), detp = list( full_name = "diethyl thiophosphate", @@ -47,17 +50,19 @@ edcs_information <- function() { pubchem_cid = "3683036", ctd_id = "C035638", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 169.16 ), dmdtp = list( full_name = "dimethyl dithiophosphate", short_name = "DMDTP", class = "OP pesticide metabolites", smiles = "CSP(=O)(O)SC", - pubchem_cid = "NA", + pubchem_cid = "36158", ctd_id = "Unsure", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 158.18 ), dmp = list( full_name = "dimethyl phosphate", @@ -67,7 +72,8 @@ edcs_information <- function() { pubchem_cid = "13134", ctd_id = "C007477", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 126.05 ), dmtp = list( full_name = "dimethyl thiophosphate", @@ -77,7 +83,8 @@ edcs_information <- function() { pubchem_cid = "168140", ctd_id = "C040340", exposome_explorer_id = "NA", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 142.12 ), bpa = list( full_name = "bisphenol A", @@ -87,7 +94,8 @@ edcs_information <- function() { pubchem_cid = "6623", ctd_id = "C006780", exposome_explorer_id = "1418", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 228.29 ), etpa = list( full_name = "ethyl-paraben", @@ -97,7 +105,8 @@ edcs_information <- function() { pubchem_cid = "8434", ctd_id = "C012313", exposome_explorer_id = "1422", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 166.17 ), mepa = list( full_name = "methyl-paraben", @@ -107,7 +116,8 @@ edcs_information <- function() { pubchem_cid = "7456", ctd_id = "C015358", exposome_explorer_id = "1421", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 152.15 ), bupa = list( full_name = "n‑butyl‑paraben", @@ -117,7 +127,8 @@ edcs_information <- function() { pubchem_cid = "7184", ctd_id = "C038091", exposome_explorer_id = "1424", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 194.23 ), oxbe = list( full_name = "oxybenzone", @@ -127,7 +138,8 @@ edcs_information <- function() { pubchem_cid = "4632", ctd_id = "C005290", exposome_explorer_id = "1419", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 228.24 ), prpa = list( full_name = "propyl-paraben", @@ -137,7 +149,8 @@ edcs_information <- function() { pubchem_cid = "7175", ctd_id = "C006068", exposome_explorer_id = "1423", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 180.20 ), trcs = list( full_name = "triclosan", @@ -147,7 +160,8 @@ edcs_information <- function() { pubchem_cid = "5564", ctd_id = "D014260", exposome_explorer_id = "1420", - parental_compound = "NA" + parental_compound = "NA", + molar_mass = 289.5 ), mbzp = list( full_name = "mono benzyl phthalate", @@ -157,7 +171,8 @@ edcs_information <- function() { pubchem_cid = "31736", ctd_id = "C103325", exposome_explorer_id = "1397", - parental_compound = "BBzP" + parental_compound = "BBzP", + molar_mass = 256.25 ), mecpp = list( full_name = "mono‑2‑ethyl 5‑carboxypentyl phthalate", @@ -167,7 +182,8 @@ edcs_information <- function() { pubchem_cid = "148386", ctd_id = "C051450", exposome_explorer_id = "1403", - parental_compound = "DEHP" + parental_compound = "DEHP", + molar_mass = 308.33 ), mehhp = list( full_name = "mono‑2‑ethyl‑5‑hydroxyhexyl phthalate", @@ -177,7 +193,8 @@ edcs_information <- function() { pubchem_cid = "170295", ctd_id = "C479069", exposome_explorer_id = "1402", - parental_compound = "DEHP" + parental_compound = "DEHP", + molar_mass = 294.34 ), meohp = list( full_name = "mono‑2‑ethyl‑5‑oxohexyl phthalate", @@ -187,7 +204,8 @@ edcs_information <- function() { pubchem_cid = "119096", ctd_id = "C080276", exposome_explorer_id = "1401", - parental_compound = "DEHP" + parental_compound = "DEHP", + molar_mass = 292.33 ), mehp = list( full_name = "mono‑2‑ethylhexyl phthalate", @@ -197,7 +215,8 @@ edcs_information <- function() { pubchem_cid = "21924291", ctd_id = "C016599", exposome_explorer_id = "Unsure", - parental_compound = "DEHP" + parental_compound = "DEHP", + molar_mass = 277.33 ), ohminp = list( full_name = "mono‑4‑methyl‑7‑hydroxyoctyl phthalate", @@ -207,7 +226,8 @@ edcs_information <- function() { pubchem_cid = "102401880", ctd_id = "NA", exposome_explorer_id = "1451", - parental_compound = "MiNP" + parental_compound = "MiNP", + molar_mass = 308.4 ), oxominp = list( full_name = "mono‑4‑methyl‑7‑oxooctyl phthalate", @@ -217,7 +237,8 @@ edcs_information <- function() { pubchem_cid = "102401881", ctd_id = "NA", exposome_explorer_id = "1492", - parental_compound = "MiNP" + parental_compound = "MiNP", + molar_mass = 306.4 ), mibp = list( full_name = "mono‑iso‑butyl phthalate", @@ -227,7 +248,8 @@ edcs_information <- function() { pubchem_cid = "92272", ctd_id = "C575690", exposome_explorer_id = "1399", - parental_compound = "DiBP" + parental_compound = "DiBP", + molar_mass = 222.24 ), mnbp = list( full_name = "mono‑n‑butyl phthalate", @@ -237,7 +259,8 @@ edcs_information <- function() { pubchem_cid = "8575", ctd_id = "C028577", exposome_explorer_id = "1398", - parental_compound = "DnBP" + parental_compound = "DnBP", + molar_mass = 222.24 ), mep = list( full_name = "monoethyl phthalate", @@ -247,18 +270,25 @@ edcs_information <- function() { pubchem_cid = "75318", ctd_id = "C581825", exposome_explorer_id = "1396", - parental_compound = "DEP" + parental_compound = "DEP", + molar_mass = 194.18 ) ) edcs_info_df <- stack(edcs_info) edcs_info_df$col_names <- .names - edcs_info_df <- tidylog::pivot_wider(edcs_info_df, - names_from = col_names, - values_from = values + edcs_info_df <- tidylog::pivot_wider( + edcs_info_df, + names_from = col_names, + values_from = values ) - edcs_info_df <- tidylog::rename(edcs_info_df, - chem_id = ind + edcs_info_df <- tidylog::rename( + edcs_info_df, + chem_id = ind + ) + + assertthat::assert_that( + length(unique(edcs_info_df$pubchem_cid)) == length(edcs_info_df$pubchem_cid) ) return(edcs_info_df) diff --git a/renv.lock b/renv.lock index d453c81..328df8b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,26 +1,26 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { "Name": "BioCsoft", - "URL": "https://bioconductor.org/packages/3.18/bioc" + "URL": "https://bioconductor.org/packages/3.19/bioc" }, { "Name": "BioCann", - "URL": "https://bioconductor.org/packages/3.18/data/annotation" + "URL": "https://bioconductor.org/packages/3.19/data/annotation" }, { "Name": "BioCexp", - "URL": "https://bioconductor.org/packages/3.18/data/experiment" + "URL": "https://bioconductor.org/packages/3.19/data/experiment" }, { "Name": "BioCworkflows", - "URL": "https://bioconductor.org/packages/3.18/workflows" + "URL": "https://bioconductor.org/packages/3.19/workflows" }, { "Name": "BioCbooks", - "URL": "https://bioconductor.org/packages/3.18/books" + "URL": "https://bioconductor.org/packages/3.19/books" }, { "Name": "CRAN", @@ -29,7 +29,7 @@ ] }, "Bioconductor": { - "Version": "3.18" + "Version": "3.19" }, "Packages": { "AsioHeaders": { @@ -41,13 +41,13 @@ }, "BiocManager": { "Package": "BiocManager", - "Version": "1.30.22", + "Version": "1.30.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + "Hash": "47e968dfe563c1b22c2e20a067ec21d5" }, "DEoptimR": { "Package": "DEoptimR", @@ -59,11 +59,21 @@ ], "Hash": "72f87e0092e39384aee16df8d67d7410" }, + "Deriv": { + "Package": "Deriv", + "Version": "4.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "methods" + ], + "Hash": "bc727aba82bcda74db0bbe188ec6757c" + }, "MASS": { "Package": "MASS", - "Version": "7.3-60.0.1", + "Version": "7.3-61", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "grDevices", @@ -72,11 +82,11 @@ "stats", "utils" ], - "Hash": "b765b28387acc8ec9e9c1530713cb19c" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-5", + "Version": "1.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -89,7 +99,7 @@ "stats", "utils" ], - "Hash": "8c7115cd3a0e048bda2a7cd110549f7a" + "Hash": "1920b2f11133b12350024297d8a4ff4a" }, "MatrixModels": { "Package": "MatrixModels", @@ -126,18 +136,18 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.6.6.1", + "Version": "14.0.0-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -147,11 +157,11 @@ "stats", "utils" ], - "Hash": "d2b60e0a15d73182a3a766ff0a7d0d7f" + "Hash": "a711769be34214addf7805278b72d56b" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.4", + "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -160,7 +170,7 @@ "stats", "utils" ], - "Hash": "acb0a5bf38490f26ab8661b467f4f53a" + "Hash": "df49e3306f232ec28f1604e36a202847" }, "Rttf2pt1": { "Package": "Rttf2pt1", @@ -174,7 +184,7 @@ }, "SparseM": { "Package": "SparseM", - "Version": "1.81", + "Version": "1.84-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -184,7 +194,7 @@ "stats", "utils" ], - "Hash": "2042cd9759cc89a453c4aefef0ce9aae" + "Hash": "e78499cbcbbca98200254bd171379165" }, "TSP": { "Package": "TSP", @@ -221,7 +231,7 @@ }, "V8": { "Package": "V8", - "Version": "4.4.1", + "Version": "4.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -230,7 +240,7 @@ "jsonlite", "utils" ], - "Hash": "435359b59b8a9b8f9235135da471ea3c" + "Hash": "ca98390ad1cef2a5a609597b49d3d042" }, "VIM": { "Package": "VIM", @@ -263,12 +273,11 @@ }, "WeightIt": { "Package": "WeightIt", - "Version": "0.14.2", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "backports", "chk", "cobalt", "crayon", @@ -277,7 +286,7 @@ "stats", "utils" ], - "Hash": "30092d55749705627984e4d836032c0f" + "Hash": "e8deaed1b614f41dfaf7b50ec145f7d5" }, "abind": { "Package": "abind", @@ -313,24 +322,19 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" + "Hash": "e1e1b9d75c37401117b636b7ae50827a" }, "badger": { "Package": "badger", - "Version": "0.2.3.002", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteRepo": "badger", - "RemoteUsername": "GuangchuangYu", - "RemoteRef": "HEAD", - "RemoteSha": "e8a542c95d847c084f66eccc841c3c067c7291bb", + "Version": "0.2.4", + "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "desc", @@ -338,7 +342,7 @@ "rvcheck", "usethis" ], - "Hash": "b9012bbcb504c2e5dca1caec6d7aef74" + "Hash": "1646e3fbd4138f3e3e2cf2f686c73501" }, "base64enc": { "Package": "base64enc", @@ -352,7 +356,7 @@ }, "bayestestR": { "Package": "bayestestR", - "Version": "0.13.1", + "Version": "0.13.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -364,7 +368,7 @@ "stats", "utils" ], - "Hash": "61f643ea5ee9fe0e70ab0246340b3c2e" + "Hash": "4a6a2eebe2db1dfb1c792c4ed91e73dc" }, "bigD": { "Package": "bigD", @@ -409,7 +413,7 @@ }, "bookdown": { "Package": "bookdown", - "Version": "0.37", + "Version": "0.40", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -422,11 +426,11 @@ "xfun", "yaml" ], - "Hash": "b1b1c3be5c75309f6107726fa58ee20c" + "Hash": "896a79478a50c78fb035a37148638f4e" }, "boot": { "Package": "boot", - "Version": "1.3-28.1", + "Version": "1.3-30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -434,28 +438,27 @@ "graphics", "stats" ], - "Hash": "9a052fbcbe97a98ceb18dbfd30ebd96e" + "Hash": "96abeed416a286d4a0f52e550b612343" }, "brio": { "Package": "brio", - "Version": "1.1.4", + "Version": "1.1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "68bd2b066e1fe780bbf62fc8bcc36de3" + "Hash": "c1ee497a6d999947c2c224ae46799b1a" }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -465,11 +468,11 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "broom.helpers": { "Package": "broom.helpers", - "Version": "1.14.0", + "Version": "1.15.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -486,17 +489,18 @@ "tibble", "tidyr" ], - "Hash": "ea30eb5d9412a4a5c2740685f680cd49" + "Hash": "768cae43c3da698d6b11763777301e43" }, "bslib": { "Package": "bslib", - "Version": "0.6.1", + "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "cachem", + "fastmap", "grDevices", "htmltools", "jquerylib", @@ -507,7 +511,7 @@ "rlang", "sass" ], - "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" + "Hash": "8644cc53f43828f19133548195d7e59e" }, "ca": { "Package": "ca", @@ -521,18 +525,18 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -541,7 +545,7 @@ "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" }, "car": { "Package": "car", @@ -579,7 +583,7 @@ }, "chk": { "Package": "chk", - "Version": "0.9.1", + "Version": "0.9.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -589,7 +593,7 @@ "rlang", "tools" ], - "Hash": "426a04600c755952486b5242e55e3baf" + "Hash": "10a1261a7dfd075139d7f7aac4301110" }, "class": { "Package": "class", @@ -606,14 +610,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.2", + "Version": "3.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", @@ -648,7 +652,7 @@ }, "cobalt": { "Package": "cobalt", - "Version": "4.5.3", + "Version": "4.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -665,17 +669,17 @@ "stats", "utils" ], - "Hash": "14d2f9b891d7ddf016a7dcfc64b1d5eb" + "Hash": "788ae7b7ffee941a95c6201fccd62504" }, "codetools": { "Package": "codetools", - "Version": "0.2-19", + "Version": "0.2-20", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "c089a619a7fae175d149d89164f8c7d8" + "Hash": "61e097f35917d342622f21cdc79c256e" }, "colorspace": { "Package": "colorspace", @@ -693,10 +697,10 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.9.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "d691c61bff84bd63c383874d2d0c3307" + "Hash": "5d8225445acb167abf7797de48b2ee3c" }, "corrr": { "Package": "corrr", @@ -716,6 +720,23 @@ ], "Hash": "2fb521ffc0592c3c47d1d7e3b0cba2d0" }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "ggplot2", + "grDevices", + "grid", + "gtable", + "methods", + "rlang", + "scales" + ], + "Hash": "8ef2084dd7d28847b374e55440e4f8cb" + }, "cpp11": { "Package": "cpp11", "Version": "0.4.7", @@ -728,7 +749,7 @@ }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -736,7 +757,7 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "credentials": { "Package": "credentials", @@ -754,7 +775,7 @@ }, "crul": { "Package": "crul", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -765,17 +786,17 @@ "mime", "urltools" ], - "Hash": "1eb00a531331c91d970f3af74b75321f" + "Hash": "22e70c5046981d39b7bf7af74433e396" }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "5.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" }, "dagitty": { "Package": "dagitty", @@ -798,18 +819,18 @@ }, "data.table": { "Package": "data.table", - "Version": "1.14.10", + "Version": "1.15.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "6ea17a32294d8ca00455825ab0cf71b9" + "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" }, "datawizard": { "Package": "datawizard", - "Version": "0.9.1", + "Version": "0.12.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -818,7 +839,7 @@ "stats", "utils" ], - "Hash": "51cf8172b52cfa5b4b988c73c37accfa" + "Hash": "4070785c656b9ded5d0ed5db387a96d5" }, "desc": { "Package": "desc", @@ -850,25 +871,20 @@ }, "digest": { "Package": "digest", - "Version": "0.6.34", + "Version": "0.6.36", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "Hash": "fd6824ad91ede64151e93af67df6376b" }, "dlookr": { "Package": "dlookr", "Version": "0.6.3", - "Source": "GitHub", - "RemoteType": "github", - "RemoteUsername": "choonghyunryu", - "RemoteRepo": "dlookr", - "RemoteRef": "HEAD", - "RemoteSha": "8330b29c46b3873807edf794111a3f9125175aa9", - "RemoteHost": "api.github.com", + "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "dplyr", @@ -895,7 +911,7 @@ "tidyselect", "utils" ], - "Hash": "607c5a11a939a72e50f56fc60aac51b7" + "Hash": "ea7cac43c7ff2bcf58b70f59f70e2ff4" }, "dlstats": { "Package": "dlstats", @@ -913,9 +929,33 @@ ], "Hash": "e9ba1c73457c25b19b94bd71eceb38ab" }, + "doBy": { + "Package": "doBy", + "Version": "4.6.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Deriv", + "MASS", + "Matrix", + "R", + "boot", + "broom", + "cowplot", + "dplyr", + "ggplot2", + "methods", + "microbenchmark", + "modelr", + "rlang", + "tibble", + "tidyr" + ], + "Hash": "a9b56885b9596c284168df26d6179c40" + }, "downlit": { "Package": "downlit", - "Version": "0.4.3", + "Version": "0.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -931,7 +971,7 @@ "withr", "yaml" ], - "Hash": "14fa1f248b60ed67e1f5418391a17b14" + "Hash": "45a6a596bf0108ee1ff16a040a2df897" }, "dplyr": { "Package": "dplyr", @@ -972,27 +1012,16 @@ ], "Hash": "4ef372b716824753719a8a38b258442d" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "0.24.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" }, "extrafont": { "Package": "extrafont", @@ -1032,17 +1061,17 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fontBitstreamVera": { "Package": "fontBitstreamVera", @@ -1119,14 +1148,14 @@ }, "fs": { "Package": "fs", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, "gclus": { "Package": "gclus", @@ -1141,7 +1170,7 @@ }, "gdtools": { "Package": "gdtools", - "Version": "0.3.5", + "Version": "0.3.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1154,7 +1183,7 @@ "systemfonts", "tools" ], - "Hash": "9df1d2b4f6cbc92ce6961d3f10156125" + "Hash": "b53e23731a5946448ad888efca14d2df" }, "generics": { "Package": "generics", @@ -1169,7 +1198,7 @@ }, "gert": { "Package": "gert", - "Version": "2.0.1", + "Version": "2.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1180,7 +1209,7 @@ "sys", "zip" ], - "Hash": "f70d3fe2d9e7654213a946963d1591eb" + "Hash": "bdc909d9f16e2478d615b0e6a7330435" }, "gfonts": { "Package": "gfonts", @@ -1201,7 +1230,7 @@ }, "ggdag": { "Package": "ggdag", - "Version": "0.2.10", + "Version": "0.2.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1221,11 +1250,11 @@ "tibble", "tidygraph" ], - "Hash": "07e9bed17027af3a3dfe3a1faecce837" + "Hash": "c923747c35d5aa953cc6d2e7cd7bfb20" }, "ggforce": { "Package": "ggforce", - "Version": "0.4.1", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1250,22 +1279,23 @@ "vctrs", "withr" ], - "Hash": "a06503f54e227f79b45a72df2946a2d2" + "Hash": "384b388bd9155468d2c851846ee69f9f" }, "ggfun": { "Package": "ggfun", - "Version": "0.1.4", + "Version": "0.1.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", + "dplyr", "ggplot2", "grid", "rlang", "utils" ], - "Hash": "91780e07f1d631a1152835b4e25c66b9" + "Hash": "4fca342cc17bb91af2a279146bc57fef" }, "ggimage": { "Package": "ggimage", @@ -1303,7 +1333,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.4", + "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1324,7 +1354,7 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" }, "ggplotify": { "Package": "ggplotify", @@ -1344,24 +1374,23 @@ }, "ggraph": { "Package": "ggraph", - "Version": "2.1.0", + "Version": "2.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "MASS", "R", - "Rcpp", "cli", - "digest", + "cpp11", "dplyr", "ggforce", "ggplot2", "ggrepel", "graphlayouts", "grid", - "gtable", "igraph", "lifecycle", + "memoise", "rlang", "scales", "stats", @@ -1371,7 +1400,7 @@ "viridis", "withr" ], - "Hash": "62672fd99df5df5814f442e9cd5ec29b" + "Hash": "1f5d21a9e1f84b4a81ddacb8f052ca61" }, "ggrepel": { "Package": "ggrepel", @@ -1391,19 +1420,21 @@ }, "gh": { "Package": "gh", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "gitcreds", + "glue", "httr2", "ini", "jsonlite", + "lifecycle", "rlang" ], - "Hash": "03533b1c875028233598f848fda44c4c" + "Hash": "fbbbc48eba7a6626a08bb365e44b563b" }, "gitcreds": { "Package": "gitcreds", @@ -1461,7 +1492,7 @@ }, "graphlayouts": { "Package": "graphlayouts", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1470,7 +1501,7 @@ "RcppArmadillo", "igraph" ], - "Hash": "5e9e4cd284ff8abba3cfc43268e3ddd5" + "Hash": "d329345a6a37666ca3f18f3b3c1347b7" }, "gridExtra": { "Package": "gridExtra", @@ -1500,7 +1531,7 @@ }, "gt": { "Package": "gt", - "Version": "0.10.1", + "Version": "0.11.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1526,13 +1557,13 @@ "vctrs", "xml2" ], - "Hash": "03009c105dfae79460b8eb9d8cf791e4" + "Hash": "3470c2eb1123db6a2c54ec812de38284" }, "gtable": { "Package": "gtable", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cli", @@ -1541,7 +1572,7 @@ "lifecycle", "rlang" ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" }, "gtsummary": { "Package": "gtsummary", @@ -1625,14 +1656,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -1650,7 +1681,7 @@ }, "hrbrthemes": { "Package": "hrbrthemes", - "Version": "0.8.0", + "Version": "0.8.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1660,31 +1691,28 @@ "ggplot2", "grDevices", "grid", - "htmltools", - "knitr", "magrittr", - "rmarkdown", "scales", - "tools" + "tools", + "utils" ], - "Hash": "0d1257948f016840ad90320ed19c8c7d" + "Hash": "c115b4507f9fc1c754649e1d5899c46d" }, "htmltools": { "Package": "htmltools", - "Version": "0.5.7", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -1710,7 +1738,7 @@ }, "httpuv": { "Package": "httpuv", - "Version": "1.6.13", + "Version": "1.6.15", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1721,26 +1749,11 @@ "promises", "utils" ], - "Hash": "d23d2879001f3d82ee9dc38a9ef53c4c" - }, - "httr": { - "Package": "httr", - "Version": "1.4.7", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "curl", - "jsonlite", - "mime", - "openssl" - ], - "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" }, "httr2": { "Package": "httr2", - "Version": "1.0.0", + "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1757,11 +1770,11 @@ "vctrs", "withr" ], - "Hash": "e2b30f1fc039a0bab047dd52bb20ef71" + "Hash": "320c8fe23fcb25a6690ef7bdb6a3a705" }, "igraph": { "Package": "igraph", - "Version": "1.6.0", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1777,9 +1790,10 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "eef74fe28b747e52288ea9e1d3600034" + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" }, "ini": { "Package": "ini", @@ -1790,7 +1804,7 @@ }, "insight": { "Package": "insight", - "Version": "0.19.7", + "Version": "0.20.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1799,7 +1813,7 @@ "stats", "utils" ], - "Hash": "750aba9b42391da33ac290b71a749023" + "Hash": "74a0751aafb4d4bc140531e46deda4ab" }, "isoband": { "Package": "isoband", @@ -1870,13 +1884,12 @@ }, "kableExtra": { "Package": "kableExtra", - "Version": "1.3.4", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "digest", - "glue", "grDevices", "graphics", "htmltools", @@ -1884,21 +1897,19 @@ "magrittr", "rmarkdown", "rstudioapi", - "rvest", "scales", "stats", "stringr", "svglite", "tools", "viridisLite", - "webshot", "xml2" ], - "Hash": "49b625e6aabe4c5f091f5850aba8ff78" + "Hash": "532d16304274c23c8563f94b79351c86" }, "knitr": { "Package": "knitr", - "Version": "1.45", + "Version": "1.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1910,7 +1921,7 @@ "xfun", "yaml" ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" + "Hash": "acf380f300c721da9fde7df115a5f86f" }, "labeling": { "Package": "labeling", @@ -1925,7 +1936,7 @@ }, "labelled": { "Package": "labelled", - "Version": "2.12.0", + "Version": "2.13.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1936,13 +1947,14 @@ "rlang", "stringr", "tidyr", + "tidyselect", "vctrs" ], - "Hash": "1ec27c624ece6c20431e9249bd232797" + "Hash": "ad4b6d757624221aec6220b8c78defeb" }, "laeken": { "Package": "laeken", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1950,7 +1962,7 @@ "R", "boot" ], - "Hash": "c925bf1563ee407d4ced4f3b3cf2ba5f" + "Hash": "7275da17901f4fea3f8dadc5a25e5f29" }, "later": { "Package": "later", @@ -1965,7 +1977,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-5", + "Version": "0.22-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1976,7 +1988,7 @@ "stats", "utils" ], - "Hash": "7c5e89f04e72d6611c77451f6331a091" + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" }, "lifecycle": { "Package": "lifecycle", @@ -1993,7 +2005,7 @@ }, "lme4": { "Package": "lme4", - "Version": "1.1-35.1", + "Version": "1.1-35.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2015,7 +2027,7 @@ "stats", "utils" ], - "Hash": "07fb0c5b727b15b0ce40feb641498e4e" + "Hash": "16a08fc75007da0d08e0c0388c7c33e6" }, "lmtest": { "Package": "lmtest", @@ -2045,7 +2057,7 @@ }, "magick": { "Package": "magick", - "Version": "2.8.2", + "Version": "2.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2053,7 +2065,7 @@ "curl", "magrittr" ], - "Hash": "87da0066dd0d7b1a95c461abfbf10411" + "Hash": "63adf42f6fa0fca09999a328e1ae8204" }, "magrittr": { "Package": "magrittr", @@ -2067,7 +2079,7 @@ }, "markdown": { "Package": "markdown", - "Version": "1.12", + "Version": "1.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2076,7 +2088,7 @@ "utils", "xfun" ], - "Hash": "765cf53992401b3b6c297b69e1edb8bd" + "Hash": "074efab766a9d6360865ad39512f2a7e" }, "memoise": { "Package": "memoise", @@ -2133,6 +2145,17 @@ ], "Hash": "da3b0891ad90d22484190996c4100f5e" }, + "microbenchmark": { + "Package": "microbenchmark", + "Version": "1.4.10", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "graphics", + "stats" + ], + "Hash": "db81b552e393ed092872cf7023469bc2" + }, "mime": { "Package": "mime", "Version": "0.12", @@ -2145,13 +2168,13 @@ }, "minqa": { "Package": "minqa", - "Version": "1.2.6", + "Version": "1.2.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Rcpp" ], - "Hash": "f48238f8d4740426ca12f53f27d004dd" + "Hash": "aba060ef3c097b26a4d304ea39d87f32" }, "mitml": { "Package": "mitml", @@ -2190,29 +2213,29 @@ }, "munsell": { "Package": "munsell", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "colorspace", "methods" ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Hash": "4fd8900853b746af55b81fda99da7695" }, "mvtnorm": { "Package": "mvtnorm", - "Version": "1.2-4", + "Version": "1.2-5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "17e96668f44a28aef0981d9e17c49b59" + "Hash": "4d1891e59ac7a12b4e7e8a69349125f1" }, "naniar": { "Package": "naniar", - "Version": "1.0.0", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2223,6 +2246,7 @@ "forcats", "ggplot2", "glue", + "lifecycle", "magrittr", "norm", "purrr", @@ -2234,13 +2258,13 @@ "viridis", "visdat" ], - "Hash": "3a684e715cebd023880a6171e35cd02c" + "Hash": "74d1b68ee4d1e076dee034a9ef3acd41" }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-165", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "graphics", @@ -2248,17 +2272,14 @@ "stats", "utils" ], - "Hash": "a623a2239e642806158bc4dc3f51565d" + "Hash": "2769a88be217841b1f33ed469675c3cc" }, "nloptr": { "Package": "nloptr", - "Version": "2.0.3", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", - "Requirements": [ - "testthat" - ], - "Hash": "277c67a08f358f42b6a77826e4492f79" + "Hash": "27550641889a3abf3aec4d91186311ec" }, "nnet": { "Package": "nnet", @@ -2294,13 +2315,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.1", + "Version": "2.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" + "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e" }, "ordinal": { "Package": "ordinal", @@ -2344,18 +2365,16 @@ "Version": "1.9", "Source": "Repository", "Repository": "CRAN", - "Hash": "495d032ad6bfc725f37ce89e3d6dadb2" + "Requirements": [ + "R" + ], + "Hash": "aefe2753a8e7277e0fdd6d1d08d1692e" }, "patchwork": { "Package": "patchwork", - "Version": "1.2.0.9000", - "Source": "GitHub", - "RemoteType": "github", - "RemoteUsername": "thomasp85", - "RemoteRepo": "patchwork", - "RemoteRef": "HEAD", - "RemoteSha": "d9437579a1fbbbfe20da0e4d44814008c1b98bb2", - "RemoteHost": "api.github.com", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "cli", "ggplot2", @@ -2367,11 +2386,11 @@ "stats", "utils" ], - "Hash": "f31f35b7274a2985f79d4ff51df2d21c" + "Hash": "9c8ab14c00ac07e9e04d1664c0b74486" }, "pbkrtest": { "Package": "pbkrtest", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2379,17 +2398,17 @@ "Matrix", "R", "broom", + "doBy", "dplyr", "lme4", "methods", - "numDeriv", - "parallel" + "numDeriv" ], - "Hash": "3b5b99f4d3f067bb9c1d59317d071370" + "Hash": "938e6bbc4ac57534f8b43224506a8966" }, "performance": { "Package": "performance", - "Version": "0.10.8", + "Version": "0.12.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2397,11 +2416,10 @@ "bayestestR", "datawizard", "insight", - "methods", "stats", "utils" ], - "Hash": "92873fb57cc5b73fe2aa0b09056a789a" + "Hash": "6d0d9762077b82869a0ea9b17787b01e" }, "permute": { "Package": "permute", @@ -2433,7 +2451,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.3", + "Version": "1.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2444,7 +2462,7 @@ "desc", "processx" ], - "Hash": "c0143443203205e6a2760ce553dafc24" + "Hash": "a29e8e134a460a01e0ca67a4763c595b" }, "pkgconfig": { "Package": "pkgconfig", @@ -2458,7 +2476,7 @@ }, "pkgdown": { "Package": "pkgdown", - "Version": "2.0.7", + "Version": "2.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2469,11 +2487,11 @@ "desc", "digest", "downlit", + "fontawesome", "fs", - "httr", + "httr2", "jsonlite", - "magrittr", - "memoise", + "openssl", "purrr", "ragg", "rlang", @@ -2484,28 +2502,29 @@ "xml2", "yaml" ], - "Hash": "16fa15449c930bf3a7761d3c68f8abf9" + "Hash": "0d3d789055c873f48521ce7e23c23f48" }, "pkgload": { "Package": "pkgload", - "Version": "1.3.4", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", - "crayon", "desc", "fs", "glue", + "lifecycle", "methods", "pkgbuild", + "processx", "rlang", "rprojroot", "utils", "withr" ], - "Hash": "876c618df5ae610be84356d5d7a5d124" + "Hash": "2ec30ffbeec83da57655b850cf2d3e0e" }, "plyr": { "Package": "plyr", @@ -2520,13 +2539,13 @@ }, "polyclip": { "Package": "polyclip", - "Version": "1.10-6", + "Version": "1.10-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "436542aadb70675e361cf359285af7c7" + "Hash": "5879bf5aae702ffef0a315c44328f984" }, "praise": { "Package": "praise", @@ -2547,7 +2566,7 @@ }, "processx": { "Package": "processx", - "Version": "3.8.3", + "Version": "3.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2556,7 +2575,7 @@ "ps", "utils" ], - "Hash": "82d48b1aec56084d9438dbf98087a7e9" + "Hash": "0c90a7d71988856bad2a2a45dd871bb9" }, "progress": { "Package": "progress", @@ -2574,7 +2593,7 @@ }, "promises": { "Package": "promises", - "Version": "1.2.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2586,7 +2605,7 @@ "rlang", "stats" ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" + "Hash": "434cd5388a3979e74be5c219bcd6e77d" }, "proxy": { "Package": "proxy", @@ -2602,14 +2621,14 @@ }, "ps": { "Package": "ps", - "Version": "1.7.6", + "Version": "1.7.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" + "Hash": "878b467580097e9c383acbb16adab57a" }, "purrr": { "Package": "purrr", @@ -2635,7 +2654,7 @@ }, "quantreg": { "Package": "quantreg", - "Version": "5.97", + "Version": "5.98", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2649,18 +2668,18 @@ "stats", "survival" ], - "Hash": "1bbc97f7d637ab3917c514a69047b2c1" + "Hash": "017561f17632c065388b7062da030952" }, "ragg": { "Package": "ragg", - "Version": "1.2.7", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "90a1b8b7e518d7f90480d56453b4d062" + "Hash": "e3087db406e079a8a2fd87f413918ed3" }, "ranger": { "Package": "ranger", @@ -2687,13 +2706,13 @@ }, "reactR": { "Package": "reactR", - "Version": "0.5.0", + "Version": "0.6.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "htmltools" ], - "Hash": "c9014fd1a435b2d790dd506589cb24e5" + "Hash": "10f4d661c235181648a5958c02c0382a" }, "reactable": { "Package": "reactable", @@ -2756,28 +2775,28 @@ }, "renv": { "Package": "renv", - "Version": "1.0.3", + "Version": "1.0.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "41b847654f567341725473431dd0d5ab" + "Hash": "397b7b2a265bc5a7a06852524dabae20" }, "rlang": { "Package": "rlang", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "42548638fae05fd9a9b5f3f437fbbbe2" + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.25", + "Version": "2.27", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2790,18 +2809,17 @@ "jsonlite", "knitr", "methods", - "stringr", "tinytex", "tools", "utils", "xfun", "yaml" ], - "Hash": "d65e35823c817f09f4de424fcdfa812a" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "robustbase": { "Package": "robustbase", - "Version": "0.99-1", + "Version": "0.99-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2812,7 +2830,7 @@ "stats", "utils" ], - "Hash": "3adb5cc6a5cc5650cb4569204a3209c3" + "Hash": "4c409c38f09a25b228670a103e584db1" }, "rpart": { "Package": "rpart", @@ -2839,10 +2857,10 @@ }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.15.0", + "Version": "0.16.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5564500e25cffad9e22244ced1379887" + "Repository": "CRAN", + "Hash": "96710351d642b70e8f02ddeb237c46a7" }, "rvcheck": { "Package": "rvcheck", @@ -2857,26 +2875,6 @@ ], "Hash": "fee46a3924e5522b01138accbe6ff804" }, - "rvest": { - "Package": "rvest", - "Version": "1.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "httr", - "lifecycle", - "magrittr", - "rlang", - "selectr", - "tibble", - "withr", - "xml2" - ], - "Hash": "a4a5ac819a467808c60e36e92ddf195e" - }, "sandwich": { "Package": "sandwich", "Version": "3.1-0", @@ -2892,7 +2890,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.8", + "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2902,7 +2900,7 @@ "rappdirs", "rlang" ], - "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" + "Hash": "d53dbfddf695303ea4ad66f86e99b95d" }, "scales": { "Package": "scales", @@ -2924,22 +2922,9 @@ ], "Hash": "c19df082ba346b0ffa6f833e92de34d1" }, - "selectr": { - "Package": "selectr", - "Version": "0.4-2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "methods", - "stringr" - ], - "Hash": "3838071b66e0c566d55cc26bd6e27bf4" - }, "seriation": { "Package": "seriation", - "Version": "1.5.4", + "Version": "1.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2958,11 +2943,11 @@ "stats", "vegan" ], - "Hash": "786c381ec4c40d1425e50ace3fee54bc" + "Hash": "fa74cd2b488a535ce9864c99ebd5d92a" }, "servr": { "Package": "servr", - "Version": "0.28", + "Version": "0.30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2972,11 +2957,11 @@ "mime", "xfun" ], - "Hash": "70954f91166202e83476043dd1942071" + "Hash": "562294886e51319dfad3f3e6e61fb0b8" }, "shape": { "Package": "shape", - "Version": "1.4.6", + "Version": "1.4.6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2985,11 +2970,11 @@ "graphics", "stats" ], - "Hash": "9067f962730f58b14d8ae54ca885509f" + "Hash": "5c47e84dc0a3ca761ae1d307889e796d" }, "shiny": { "Package": "shiny", - "Version": "1.8.0", + "Version": "1.8.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2999,7 +2984,6 @@ "cachem", "commonmark", "crayon", - "ellipsis", "fastmap", "fontawesome", "glue", @@ -3019,11 +3003,11 @@ "withr", "xtable" ], - "Hash": "3a1f41807d648a908e3c7f0334bf85e6" + "Hash": "54b26646816af9960a4c64d8ceec75d6" }, "showtext": { "Package": "showtext", - "Version": "0.9-6", + "Version": "0.9-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3031,7 +3015,7 @@ "showtextdb", "sysfonts" ], - "Hash": "c0fd332d248b195bbcb94a0dfda37b0d" + "Hash": "ebc23fc796c28737ffe0a64e5404f3d1" }, "showtextdb": { "Package": "showtextdb", @@ -3056,7 +3040,7 @@ }, "sp": { "Package": "sp", - "Version": "2.1-2", + "Version": "2.1-4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3069,11 +3053,11 @@ "stats", "utils" ], - "Hash": "40a9887191d33b2521a1d741f8c8aea2" + "Hash": "75940133cca2e339afce15a586f85b11" }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3082,7 +3066,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -3103,9 +3087,9 @@ }, "survival": { "Package": "survival", - "Version": "3.5-7", + "Version": "3.7-0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "Matrix", "R", @@ -3115,7 +3099,7 @@ "stats", "utils" ], - "Hash": "b8e943d262c3da0b0febd3e04517c197" + "Hash": "5aaa9cbaf4aba20f8e06fdea1850a398" }, "svglite": { "Package": "svglite", @@ -3138,25 +3122,26 @@ }, "sysfonts": { "Package": "sysfonts", - "Version": "0.8.8", + "Version": "0.8.9", "Source": "Repository", "Repository": "CRAN", - "Hash": "7f4dac41a3e348ae12832167e6beb875" + "Hash": "7dfca1e9c5c278300b5ca6a1772072f7" }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.5", + "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "15b594369e70b975ba9f064295983499" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "testthat": { "Package": "testthat", - "Version": "3.2.1", + "Version": "3.2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3181,19 +3166,20 @@ "waldo", "withr" ], - "Hash": "4767a686ebe986e6cb01d075b3f09729" + "Hash": "3f6e7e5e2220856ff865e4834766bf2b" }, "textshaping": { "Package": "textshaping", - "Version": "0.3.7", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", @@ -3216,7 +3202,7 @@ }, "tidygraph": { "Package": "tidygraph", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3235,24 +3221,25 @@ "tools", "utils" ], - "Hash": "5c1d6e75684cd37665f7f686dad19510" + "Hash": "2149824d406f233b57b087be72c5f163" }, "tidylog": { "Package": "tidylog", - "Version": "1.0.2", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "clisymbols", "dplyr", "glue", + "rlang", "tidyr" ], - "Hash": "a55d41e241dbe858d1456d952ce3301f" + "Hash": "91b7d5e3d5c01c3877f243d47f4e8fec" }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3271,11 +3258,11 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3287,7 +3274,7 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "timechange": { "Package": "timechange", @@ -3302,13 +3289,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.49", + "Version": "0.52", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "Hash": "cfbad971a71f0e27cec22e544a08bc3b" }, "tmvtnorm": { "Package": "tmvtnorm", @@ -3339,7 +3326,7 @@ }, "tweenr": { "Package": "tweenr", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3350,7 +3337,7 @@ "rlang", "vctrs" ], - "Hash": "c16efcef4c72d3bff5e65031f3f1f841" + "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc" }, "tzdb": { "Package": "tzdb", @@ -3365,13 +3352,13 @@ }, "ucminf": { "Package": "ucminf", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "48f2c17a0f91a1669cffdc8593aa62b2" + "Hash": "e0750b911c01c3e5aaab143a86e9e478" }, "urltools": { "Package": "urltools", @@ -3388,7 +3375,7 @@ }, "usethis": { "Package": "usethis", - "Version": "2.2.2", + "Version": "2.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3415,7 +3402,7 @@ "withr", "yaml" ], - "Hash": "60e51f0b94d0324dc19e44110098fa9f" + "Hash": "d524fd42c517035027f866064417d7e6" }, "utf8": { "Package": "utf8", @@ -3460,7 +3447,7 @@ }, "vegan": { "Package": "vegan", - "Version": "2.6-4", + "Version": "2.6-6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3471,20 +3458,20 @@ "mgcv", "permute" ], - "Hash": "659fe7589b8e0b16baa49043a61a0ce0" + "Hash": "46a520e3fd3286168c3e4dc5e6fbb5b1" }, "viridis": { "Package": "viridis", - "Version": "0.6.4", + "Version": "0.6.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "ggplot2", "gridExtra", "viridisLite" ], - "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1" + "Hash": "acd96d9fa70adeea4a5a1150609b9745" }, "viridisLite": { "Package": "viridisLite", @@ -3562,22 +3549,9 @@ ], "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6" }, - "webshot": { - "Package": "webshot", - "Version": "0.5.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "callr", - "jsonlite", - "magrittr" - ], - "Hash": "16858ee1aba97f902d24049d4a44ef16" - }, "websocket": { "Package": "websocket", - "Version": "1.4.1", + "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3586,7 +3560,7 @@ "cpp11", "later" ], - "Hash": "76e0d400757e318cca33def29ccebbc2" + "Hash": "e77c5569354172d0d04d54a9dec89e33" }, "whisker": { "Package": "whisker", @@ -3609,14 +3583,15 @@ }, "xfun": { "Package": "xfun", - "Version": "0.41", + "Version": "0.46", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "grDevices", "stats", "tools" ], - "Hash": "460a5e0fe46a80ef87424ad216028014" + "Hash": "00ce32f398db0415dde61abfef11300c" }, "xml2": { "Package": "xml2", @@ -3645,14 +3620,14 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.9", "Source": "Repository", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Hash": "9cb28d11799d93c953f852083d55ee9e" }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3665,14 +3640,14 @@ "tools", "utils" ], - "Hash": "5d48e23c846e9c2cd6055d652590a628" + "Hash": "60ee2aaa179dc282e9fa7367bad76e89" }, "zip": { "Package": "zip", - "Version": "2.3.0", + "Version": "2.3.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "d98c94dacb7e0efcf83b0a133a705504" + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" }, "zoo": { "Package": "zoo", diff --git a/renv/activate.R b/renv/activate.R index cb5401f..d13f993 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.7" attr(version, "sha") <- NULL # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -31,6 +33,14 @@ 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 +60,22 @@ 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") @@ -108,6 +131,21 @@ local({ } + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } @@ -610,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -801,24 +842,23 @@ local({ # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] + sha = if (dev) description[["RemoteSha"]] ) - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE @@ -1041,7 +1081,7 @@ 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 +1090,7 @@ 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 +1103,14 @@ 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 +1158,14 @@ 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 +1192,7 @@ 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/tests/testthat.R b/tests/testthat.R index 1132027..d8dc13e 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -7,6 +7,6 @@ # * https://testthat.r-lib.org/articles/special-files.html library(testthat) -library(myphd) +# library(myphd) -test_check("myphd") +# test_check("myphd")