R Under development (unstable) (2026-03-17 r89645 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #! /usr/bin/env Rscript > ## This runs testme test script inst/testme/test-api.R > ## Don't edit - it was autogenerated by inst/testme/deploy.R > futurize:::testme("api") Test 'api' ... chr "none" > library(futurize) Loading required package: future > options(futurize.debug = TRUE) > message("futurize(NA):") futurize(NA): > res <- futurize(NA) [16:11:32.952] futurize() ... [16:11:32.954] | transpile() ... [16:11:32.955] | transpile() ... done [16:11:32.956] futurize() ... done > print(res) [1] TRUE > stopifnot(isTRUE(res)) > message("futurize(FALSE):") futurize(FALSE): > res <- futurize(FALSE) [16:11:32.958] futurize() ... [16:11:32.959] | transpile() ... [16:11:32.960] | transpile() ... done [16:11:32.961] futurize() ... done > print(res) [1] TRUE > stopifnot(isTRUE(res)) > message("futurize(TRUE):") futurize(TRUE): > res <- futurize(TRUE) [16:11:32.963] futurize() ... [16:11:32.967] | transpile() ... [16:11:32.968] | transpile() ... done [16:11:32.969] futurize() ... done > print(res) [1] FALSE > stopifnot(isFALSE(res)) > if (requireNamespace("future.apply", quietly = TRUE)) { + message("futurize(when = FALSE):") + y_truth <- lapply(1:3, identity) + y <- f .... [TRUNCATED] futurize(when = FALSE): [16:11:32.971] futurize() ... [16:11:32.971] | transpile() ... [16:11:32.972] | : Evaluate call expression [16:11:32.973] | transpile() ... done [16:11:32.974] futurize() ... done [16:11:32.975] futurize() ... [16:11:32.976] | transpile() ... [16:11:32.978] | : get_transpiler() ... [16:11:32.979] | : . Finding call to be transpiled ... [16:11:32.980] | : . | descend_wrappers() ... [16:11:32.981] | : . | : Call: [16:11:32.982] | : . | : lapply [16:11:32.983] | : . | : parse_call() ... [16:11:32.984] | : . | : . Function: lapply(...) [16:11:32.985] | : . | : . Locate function ... [16:11:32.986] | : . | : . | Function located in: 'base' [16:11:32.987] | : . | : . Locate function ... done [16:11:32.988] | : . | : parse_call() ... done [16:11:32.989] | : . | descend_wrappers() ... done [16:11:32.990] | : . | parse_call() ... [16:11:32.991] | : . | : Function: lapply(...) [16:11:32.992] | : . | : Locate function ... [16:11:32.993] | : . | : . Function located in: 'base' [16:11:32.994] | : . | : Locate function ... done [16:11:32.995] | : . | parse_call() ... done [16:11:32.996] | : . | Position of call to be transpiled in expression: c(1) [16:11:32.997] | : . | lapply [16:11:32.998] | : . Finding call to be transpiled ... done [16:11:32.999] | : . Locating 'futurize::add-on' transpiler for base::lapply() of class 'function' ... [16:11:33.000] | : . | transpilers_for_package(action = 'make', type = 'futurize::add-on') ... [16:11:33.001] | : . | : - package: 'base' [16:11:33.002] | : . | : $fcns [16:11:33.002] | : . | : $fcns[[1]] [16:11:33.002] | : . | : function () [16:11:33.002] | : . | : { [16:11:33.002] | : . | : append_transpilers("futurize::add-on", make_addon_transpilers("base", [16:11:33.002] | : . | : "future.apply", make_options = make_options_for_future.apply)) [16:11:33.002] | : . | : append_transpilers("futurize::add-on", make_addon_transpilers("stats", [16:11:33.002] | : . | : "future.apply", make_options = make_options_for_future.apply)) [16:11:33.002] | : . | : c("future.apply") [16:11:33.002] | : . | : } [16:11:33.002] | : . | : [16:11:33.002] | : . | : [16:11:33.002] | : . | : [16:11:33.002] | : . | : [16:11:33.013] | : . | transpilers_for_package(action = 'make', type = 'futurize::add-on') ... done [16:11:33.014] | : . | Required packages: [n=1] 'future.apply' [16:11:33.015] | : . | Namespaces registered with futurize(): 'base', 'stats' [16:11:33.016] | : . | Transpiler description: base::lapply() -> future.apply::future_lapply() [16:11:33.017] | : . | Transpiler function: [16:11:33.018] | : . | function (expr, options = NULL) [16:11:33.018] | : . | { [16:11:33.018] | : . | call <- make_call("future_lapply") [16:11:33.018] | : . | fcn <- eval(call) [16:11:33.018] | : . | expr[[1]] <- call [16:11:33.018] | : . | parts <- c(as.list(expr), (function (options, fcn, defaults = NULL) [16:11:33.018] | : . | { [16:11:33.018] | : . | if (length(options) == 0L && length(defaults) == 0L) return(options) [16:11:33.018] | : . | if (is.null(defaults_base)) { [16:11:33.018] | : . | defaults_base <<- get_defaults(future.apply::future_lapply) [16:11:33.018] | : . | } [16:11:33.018] | : . | defaults <- c(defaults_base, get_defaults(fcn), defaults) [16:11:33.018] | : . | keep <- !duplicated(names(defaults), fromLast = TRUE) [16:11:33.018] | : . | defaults <- defaults[keep] [16:11:33.018] | : . | specified <- attr(options, "specified") [16:11:33.018] | : . | if (length(specified) > 0) { [16:11:33.018] | : . | specified <- sub("^chunk_size$", "chunk.size", specified) [16:11:33.018] | : . | names(options) <- sub("^chunk_size$", "chunk.size", [16:11:33.018] | : . | names(options)) [16:11:33.018] | : . | } [16:11:33.018] | : . | specified <- sprintf("future.%s", specified) [16:11:33.018] | : . | names <- setdiff(names(defaults), specified) [16:11:33.018] | : . | names(options) <- sprintf("future.%s", names(options)) [16:11:33.018] | : . | for (name in names) options[[name]] <- defaults[[name]] [16:11:33.018] | : . | keep <- intersect(names(options), names(defaults)) [16:11:33.018] | : . | options <- options[keep] [16:11:33.018] | : . | options [16:11:33.018] | : . | })(options, fcn)) [16:11:33.018] | : . | expr <- as.call(parts) [16:11:33.018] | : . | expr [16:11:33.018] | : . | } [16:11:33.018] | : . | [16:11:33.020] | : . Locating 'futurize::add-on' transpiler for base::lapply() of class 'function' ... done [16:11:33.021] | : get_transpiler() ... done [16:11:33.022] | : Transpile call expression ... [16:11:33.024] | : . future.apply::future_lapply(1:3, identity, future.seed = FALSE, [16:11:33.024] | : . future.globals = TRUE, future.stdout = TRUE, future.conditions = "condition", [16:11:33.024] | : . future.scheduling = 1, future.label = "future_lapply-%d") [16:11:33.026] | : Transpile call expression ... done [16:11:33.027] | : Evaluate transpiled call expression [16:11:33.133] | transpile() ... done [16:11:33.134] futurize() ... done [16:11:33.135] futurize() ... [16:11:33.135] | transpile() ... [16:11:33.136] | : Return call expression [16:11:33.137] | transpile() ... done [16:11:33.138] futurize() ... done lapply(1:3, identity) > res <- tryCatch(futurize(base::pi), error = identity) [16:11:33.139] futurize() ... [16:11:33.140] | transpile() ... [16:11:33.141] | : get_transpiler() ... [16:11:33.142] | : . Finding call to be transpiled ... [16:11:33.143] | : . | descend_wrappers() ... [16:11:33.144] | : . | : Call: [16:11:33.145] | : . | : `::` [16:11:33.146] | : . | : parse_call() ... [16:11:33.147] | : . | : . Function: ::(...) [16:11:33.148] | : . | : . Locate function ... [16:11:33.149] | : . | : . | Function located in: 'base' [16:11:33.149] | : . | : . Locate function ... done [16:11:33.150] | : . | : parse_call() ... done [16:11:33.151] | : . | descend_wrappers() ... done [16:11:33.152] | : . | parse_call() ... [16:11:33.153] | : . | : Function: ::(...) [16:11:33.154] | : . | : Locate function ... [16:11:33.154] | : . | : . Function located in: 'base' [16:11:33.155] | : . | : Locate function ... done [16:11:33.155] | : . | parse_call() ... done [16:11:33.156] | : . | Position of call to be transpiled in expression: c(1) [16:11:33.157] | : . | `::` [16:11:33.158] | : . Finding call to be transpiled ... done [16:11:33.195] | : . Locating 'futurize::add-on' transpiler for base::::() of class 'function' ... [16:11:33.196] | : . | Namespaces registered with futurize(): 'base', 'stats' [16:11:33.197] | : . Locating 'futurize::add-on' transpiler for base::::() of class 'function' ... done [16:11:33.197] | : get_transpiler() ... done [16:11:33.198] | transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > res <- tryCatch(futurize(quote(1 + 2)), error = identity) [16:11:33.200] | futurize() ... [16:11:33.200] | : transpile() ... [16:11:33.201] | : . get_transpiler() ... [16:11:33.202] | : . | Finding call to be transpiled ... [16:11:33.202] | : . | : descend_wrappers() ... [16:11:33.203] | : . | : . Call: [16:11:33.203] | : . | : . quote [16:11:33.204] | : . | : . parse_call() ... [16:11:33.205] | : . | : . | Function: quote(...) [16:11:33.205] | : . | : . | Locate function ... [16:11:33.206] | : . | : . | : Function located in: 'base' [16:11:33.206] | : . | : . | Locate function ... done [16:11:33.207] | : . | : . parse_call() ... done [16:11:33.207] | : . | : descend_wrappers() ... done [16:11:33.208] | : . | : parse_call() ... [16:11:33.209] | : . | : . Function: quote(...) [16:11:33.209] | : . | : . Locate function ... [16:11:33.210] | : . | : . | Function located in: 'base' [16:11:33.211] | : . | : . Locate function ... done [16:11:33.211] | : . | : parse_call() ... done [16:11:33.212] | : . | : Position of call to be transpiled in expression: c(1) [16:11:33.213] | : . | : quote [16:11:33.215] | : . | Finding call to be transpiled ... done [16:11:33.216] | : . | Locating 'futurize::add-on' transpiler for base::quote() of class 'function' ... [16:11:33.217] | : . | : Namespaces registered with futurize(): 'base', 'stats' [16:11:33.218] | : . | Locating 'futurize::add-on' transpiler for base::quote() of class 'function' ... done [16:11:33.219] | : . get_transpiler() ... done [16:11:33.220] | : transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > res <- tryCatch(futurize(futurize:::unknown), error = identity) [16:11:33.221] | : futurize() ... [16:11:33.222] | : . transpile() ... [16:11:33.223] | : . | get_transpiler() ... [16:11:33.223] | : . | : Finding call to be transpiled ... [16:11:33.224] | : . | : . descend_wrappers() ... [16:11:33.225] | : . | : . | Call: [16:11:33.225] | : . | : . | `:::` [16:11:33.226] | : . | : . | parse_call() ... [16:11:33.227] | : . | : . | : Function: :::(...) [16:11:33.228] | : . | : . | : Locate function ... [16:11:33.228] | : . | : . | : . Function located in: 'base' [16:11:33.229] | : . | : . | : Locate function ... done [16:11:33.230] | : . | : . | parse_call() ... done [16:11:33.230] | : . | : . descend_wrappers() ... done [16:11:33.231] | : . | : . parse_call() ... [16:11:33.232] | : . | : . | Function: :::(...) [16:11:33.232] | : . | : . | Locate function ... [16:11:33.233] | : . | : . | : Function located in: 'base' [16:11:33.234] | : . | : . | Locate function ... done [16:11:33.234] | : . | : . parse_call() ... done [16:11:33.235] | : . | : . Position of call to be transpiled in expression: c(1) [16:11:33.236] | : . | : . `:::` [16:11:33.238] | : . | : Finding call to be transpiled ... done [16:11:33.239] | : . | : Locating 'futurize::add-on' transpiler for base:::::() of class 'function' ... [16:11:33.240] | : . | : . Namespaces registered with futurize(): 'base', 'stats' [16:11:33.241] | : . | : Locating 'futurize::add-on' transpiler for base:::::() of class 'function' ... done [16:11:33.242] | : . | get_transpiler() ... done [16:11:33.243] | : . transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > res <- tryCatch(futurize(futurize:::`%unknown%`), + error = identity) [16:11:33.245] | : . futurize() ... [16:11:33.245] | : . | transpile() ... [16:11:33.247] | : . | : get_transpiler() ... [16:11:33.248] | : . | : . Finding call to be transpiled ... [16:11:33.249] | : . | : . | descend_wrappers() ... [16:11:33.250] | : . | : . | : Call: [16:11:33.251] | : . | : . | : `:::` [16:11:33.252] | : . | : . | : parse_call() ... [16:11:33.253] | : . | : . | : . Function: :::(...) [16:11:33.255] | : . | : . | : . Locate function ... [16:11:33.256] | : . | : . | : . | Function located in: 'base' [16:11:33.257] | : . | : . | : . Locate function ... done [16:11:33.258] | : . | : . | : parse_call() ... done [16:11:33.259] | : . | : . | descend_wrappers() ... done [16:11:33.260] | : . | : . | parse_call() ... [16:11:33.261] | : . | : . | : Function: :::(...) [16:11:33.262] | : . | : . | : Locate function ... [16:11:33.264] | : . | : . | : . Function located in: 'base' [16:11:33.265] | : . | : . | : Locate function ... done [16:11:33.266] | : . | : . | parse_call() ... done [16:11:33.267] | : . | : . | Position of call to be transpiled in expression: c(1) [16:11:33.268] | : . | : . | `:::` [16:11:33.269] | : . | : . Finding call to be transpiled ... done [16:11:33.271] | : . | : . Locating 'futurize::add-on' transpiler for base:::::() of class 'function' ... [16:11:33.272] | : . | : . | Namespaces registered with futurize(): 'base', 'stats' [16:11:33.273] | : . | : . Locating 'futurize::add-on' transpiler for base:::::() of class 'function' ... done [16:11:33.274] | : . | : get_transpiler() ... done [16:11:33.275] | : . | transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > res <- tryCatch(futurize(futurize:::futurize_supported_packages()), + error = identity) [16:11:33.277] | : . | futurize() ... [16:11:33.279] | : . | : transpile() ... [16:11:33.280] | : . | : . get_transpiler() ... [16:11:33.281] | : . | : . | Finding call to be transpiled ... [16:11:33.282] | : . | : . | : descend_wrappers() ... [16:11:33.283] | : . | : . | : . Call: [16:11:33.284] | : . | : . | : . futurize:::futurize_supported_packages [16:11:33.286] | : . | : . | : . parse_call() ... [16:11:33.287] | : . | : . | : . parse_call() ... done [16:11:33.288] | : . | : . | : descend_wrappers() ... done [16:11:33.290] | : . | : . | Finding call to be transpiled ... done [16:11:33.291] | : . | : . get_transpiler() ... done [16:11:33.292] | : . | : transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > res <- tryCatch(futurize(futurize:::import_future()), + error = identity) [16:11:33.294] | : . | : futurize() ... [16:11:33.295] | : . | : . transpile() ... [16:11:33.296] | : . | : . | get_transpiler() ... [16:11:33.297] | : . | : . | : Finding call to be transpiled ... [16:11:33.298] | : . | : . | : . descend_wrappers() ... [16:11:33.300] | : . | : . | : . | Call: [16:11:33.301] | : . | : . | : . | futurize:::import_future [16:11:33.302] | : . | : . | : . | parse_call() ... [16:11:33.303] | : . | : . | : . | parse_call() ... done [16:11:33.304] | : . | : . | : . descend_wrappers() ... done [16:11:33.306] | : . | : . | : Finding call to be transpiled ... done [16:11:33.307] | : . | : . | get_transpiler() ... done [16:11:33.308] | : . | : . transpile() ... done > print(res) > stopifnot(inherits(res, "error")) > message("*** futurize_options() - specified tracking") *** futurize_options() - specified tracking > opts <- futurize_options(seed = TRUE) > stopifnot("seed" %in% attr(opts, "specified")) > stopifnot(!("globals" %in% attr(opts, "specified"))) > opts <- futurize_options(seed = TRUE, globals = FALSE, + packages = "foo", stdout = FALSE, conditions = "warning", + scheduling = 2, chunk .... [TRUNCATED] > specified <- attr(opts, "specified") > stopifnot(all(c("seed", "globals", "packages", "stdout", + "conditions", "scheduling", "chunk_size") %in% specified)) > opts <- futurize_options(extra_opt = 42) > stopifnot("extra_opt" %in% attr(opts, "specified")) > pkgs <- futurize_supported_packages() > print(pkgs) [1] "BiocParallel" "DESeq2" "GSVA" [4] "GenomicAlignments" "Rsamtools" "SimDesign" [7] "SingleCellExperiment" "TSP" "base" [10] "boot" "caret" "crossmap" [13] "fgsea" "foreach" "fwb" [16] "gamlss" "glmmTMB" "glmnet" [19] "kernelshap" "lme4" "metafor" [22] "mgcv" "partykit" "pbapply" [25] "plyr" "purrr" "riskRegression" [28] "scater" "scuttle" "seriation" [31] "shapr" "stats" "strucchange" [34] "sva" "tm" "vegan" > for (pkg in c(pkgs, "future", "aNonExistingPackage")) { + cat(sprintf("Package %s:\n", pkg)) + fcns <- tryCatch({ + futurize::futuri .... [TRUNCATED] Package BiocParallel: [1] ".bpiterate_impl" ".bplapply_impl" ".manager" "bpaggregate" [5] "bpiterate" "bplapply" "bploop.iterate" "bploop.lapply" [9] "bpmapply" "bpvec" Package DESeq2: [1] "DESeq" "lfcShrink" "results" Package GSVA: [1] "gsvaRanks" "gsvaScores" "spatCor" Package GenomicAlignments: [1] "summarizeOverlaps" Package Rsamtools: [1] "countBam" "scanBam" Package SimDesign: [1] "SimSolve" "runArraySimulation" "runSimulation" Package SingleCellExperiment: [1] "applySCE" Package TSP: [1] "solve_TSP" Package base: [1] ".mapply" "Filter" "Map" "apply" "by" "eapply" [7] "lapply" "mapply" "replicate" "sapply" "tapply" "vapply" Package boot: [1] "boot" "censboot" "tsboot" Package caret: [1] "bag" "gafs" "nearZeroVar" "rfe" "safs" [6] "sbf" "train" Package crossmap: [1] "imap_vec" "map2_vec" "map_vec" "pmap_vec" "xmap" "xmap_arr" [7] "xmap_chr" "xmap_dbl" "xmap_dfc" "xmap_dfr" "xmap_int" "xmap_lgl" [13] "xmap_mat" "xmap_raw" "xmap_vec" "xwalk" Package fgsea: [1] "collapsePathwaysGeseca" "fgsea" "fgseaLabel" [4] "fgseaMultilevel" "fgseaSimple" "geseca" [7] "gesecaSimple" Package foreach: [1] "%do%" "%dopar%" Package fwb: [1] "fwb" "vcovFWB" Package gamlss: [1] "add1All" "add1TGD" "addterm.gamlss" "drop1All" [5] "drop1TGD" "dropterm.gamlss" "gamlssCV" Package glmmTMB: Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.19 Current TMB package version is 1.9.20 Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information) [1] "profile.glmmTMB" Package glmnet: [1] "cv.glmnet" Package kernelshap: [1] "kernelshap" "permshap" Package lme4: [1] "allFit" "bootMer" "influence.merMod" "profile.merMod" Package metafor: [1] "cooks.distance.rma.mv" "dfbetas.rma.mv" [3] "gosh.rma" "profile.rma.ls" [5] "profile.rma.mv" "profile.rma.uni" [7] "profile.rma.uni.selmodel" "rstudent.rma.mv" [9] "vif.rma" Package mgcv: [1] "bam" "predict.bam" Package partykit: [1] "cforest" "ctree_control" "mob_control" "varimp.cforest" Package pbapply: [1] "pbapply" "pbby" "pbby.data.frame" "pbby.default" [5] "pbeapply" "pblapply" "pbreplicate" "pbsapply" [9] "pbtapply" "pbvapply" "pbwalk" Package plyr: [1] "a_ply" "aaply" "adply" "alply" "d_ply" "daply" "ddply" "dlply" "l_ply" [10] "laply" "ldply" "llply" "m_ply" "maply" "mdply" "mlply" Package purrr: [1] "imap" "imap_chr" "imap_dbl" "imap_dfc" [5] "imap_dfr" "imap_int" "imap_lgl" "imap_raw" [9] "invoke_map" "invoke_map_chr" "invoke_map_dbl" "invoke_map_dfc" [13] "invoke_map_dfr" "invoke_map_int" "invoke_map_lgl" "invoke_map_raw" [17] "iwalk" "map" "map2" "map2_chr" [21] "map2_dbl" "map2_dfc" "map2_dfr" "map2_int" [25] "map2_lgl" "map2_raw" "map_at" "map_chr" [29] "map_dbl" "map_dfc" "map_dfr" "map_if" [33] "map_int" "map_lgl" "map_raw" "modify" [37] "modify_at" "modify_if" "pmap" "pmap_chr" [41] "pmap_dbl" "pmap_dfc" "pmap_dfr" "pmap_int" [45] "pmap_lgl" "pmap_raw" "pwalk" "walk" [49] "walk2" Package riskRegression: [1] "Score.list" Package scater: [1] "calculatePCA" "calculateTSNE" "calculateUMAP" [4] "getVarianceExplained" "nexprs" "plotRLE" [7] "runColDataPCA" "runTSNE" "runUMAP" Package scuttle: [1] "addPerCellQC" "addPerCellQCMetrics" [3] "addPerFeatureQC" "addPerFeatureQCMetrics" [5] "aggregateAcrossCells" "aggregateAcrossFeatures" [7] "calculateAverage" "computeGeometricFactors" [9] "computeLibraryFactors" "computeMedianFactors" [11] "computePooledFactors" "fitLinearModel" [13] "geometricSizeFactors" "librarySizeFactors" [15] "logNormCounts" "medianSizeFactors" [17] "normalizeCounts" "numDetectedAcrossCells" [19] "numDetectedAcrossFeatures" "perCellQCMetrics" [21] "perFeatureQCMetrics" "pooledSizeFactors" [23] "sumCountsAcrossCells" "sumCountsAcrossFeatures" [25] "summarizeAssayByGroup" Package seriation: [1] "seriate_best" "seriate_rep" Package shapr: [1] "explain" "explain_forecast" Package stats: [1] "kernapply" Package strucchange: [1] "breakpoints.formula" Package sva: [1] "ComBat" "read.degradation.matrix" Package tm: [1] "TermDocumentMatrix" "tm_index" "tm_map" Package vegan: [1] "adonis" "adonis2" "anosim" [4] "anova.cca" "bioenv.default" "cascadeKM" [7] "estaccumR" "mantel" "mantel.partial" [10] "metaMDSiter" "mrpp" "oecosimu" [13] "ordiareatest" "permutest.betadisper" "permutest.cca" Package future: Package aNonExistingPackage: > pkgs <- futurize_supported_packages() > for (pkg in rep(pkgs, times = 2)) { + cat(sprintf("Package %s:\n", pkg)) + fcns <- tryCatch({ + futurize::futurize_supported_functio .... [TRUNCATED] Package BiocParallel: [1] ".bpiterate_impl" ".bplapply_impl" ".manager" "bpaggregate" [5] "bpiterate" "bplapply" "bploop.iterate" "bploop.lapply" [9] "bpmapply" "bpvec" Package DESeq2: [1] "DESeq" "lfcShrink" "results" Package GSVA: [1] "gsvaRanks" "gsvaScores" "spatCor" Package GenomicAlignments: [1] "summarizeOverlaps" Package Rsamtools: [1] "countBam" "scanBam" Package SimDesign: [1] "SimSolve" "runArraySimulation" "runSimulation" Package SingleCellExperiment: [1] "applySCE" Package TSP: [1] "solve_TSP" Package base: [1] ".mapply" "Filter" "Map" "apply" "by" "eapply" [7] "lapply" "mapply" "replicate" "sapply" "tapply" "vapply" Package boot: [1] "boot" "censboot" "tsboot" Package caret: [1] "bag" "gafs" "nearZeroVar" "rfe" "safs" [6] "sbf" "train" Package crossmap: [1] "imap_vec" "map2_vec" "map_vec" "pmap_vec" "xmap" "xmap_arr" [7] "xmap_chr" "xmap_dbl" "xmap_dfc" "xmap_dfr" "xmap_int" "xmap_lgl" [13] "xmap_mat" "xmap_raw" "xmap_vec" "xwalk" Package fgsea: [1] "collapsePathwaysGeseca" "fgsea" "fgseaLabel" [4] "fgseaMultilevel" "fgseaSimple" "geseca" [7] "gesecaSimple" Package foreach: [1] "%do%" "%dopar%" Package fwb: [1] "fwb" "vcovFWB" Package gamlss: [1] "add1All" "add1TGD" "addterm.gamlss" "drop1All" [5] "drop1TGD" "dropterm.gamlss" "gamlssCV" Package glmmTMB: [1] "profile.glmmTMB" Package glmnet: [1] "cv.glmnet" Package kernelshap: [1] "kernelshap" "permshap" Package lme4: [1] "allFit" "bootMer" "influence.merMod" "profile.merMod" Package metafor: [1] "cooks.distance.rma.mv" "dfbetas.rma.mv" [3] "gosh.rma" "profile.rma.ls" [5] "profile.rma.mv" "profile.rma.uni" [7] "profile.rma.uni.selmodel" "rstudent.rma.mv" [9] "vif.rma" Package mgcv: [1] "bam" "predict.bam" Package partykit: [1] "cforest" "ctree_control" "mob_control" "varimp.cforest" Package pbapply: [1] "pbapply" "pbby" "pbby.data.frame" "pbby.default" [5] "pbeapply" "pblapply" "pbreplicate" "pbsapply" [9] "pbtapply" "pbvapply" "pbwalk" Package plyr: [1] "a_ply" "aaply" "adply" "alply" "d_ply" "daply" "ddply" "dlply" "l_ply" [10] "laply" "ldply" "llply" "m_ply" "maply" "mdply" "mlply" Package purrr: [1] "imap" "imap_chr" "imap_dbl" "imap_dfc" [5] "imap_dfr" "imap_int" "imap_lgl" "imap_raw" [9] "invoke_map" "invoke_map_chr" "invoke_map_dbl" "invoke_map_dfc" [13] "invoke_map_dfr" "invoke_map_int" "invoke_map_lgl" "invoke_map_raw" [17] "iwalk" "map" "map2" "map2_chr" [21] "map2_dbl" "map2_dfc" "map2_dfr" "map2_int" [25] "map2_lgl" "map2_raw" "map_at" "map_chr" [29] "map_dbl" "map_dfc" "map_dfr" "map_if" [33] "map_int" "map_lgl" "map_raw" "modify" [37] "modify_at" "modify_if" "pmap" "pmap_chr" [41] "pmap_dbl" "pmap_dfc" "pmap_dfr" "pmap_int" [45] "pmap_lgl" "pmap_raw" "pwalk" "walk" [49] "walk2" Package riskRegression: [1] "Score.list" Package scater: [1] "calculatePCA" "calculateTSNE" "calculateUMAP" [4] "getVarianceExplained" "nexprs" "plotRLE" [7] "runColDataPCA" "runTSNE" "runUMAP" Package scuttle: [1] "addPerCellQC" "addPerCellQCMetrics" [3] "addPerFeatureQC" "addPerFeatureQCMetrics" [5] "aggregateAcrossCells" "aggregateAcrossFeatures" [7] "calculateAverage" "computeGeometricFactors" [9] "computeLibraryFactors" "computeMedianFactors" [11] "computePooledFactors" "fitLinearModel" [13] "geometricSizeFactors" "librarySizeFactors" [15] "logNormCounts" "medianSizeFactors" [17] "normalizeCounts" "numDetectedAcrossCells" [19] "numDetectedAcrossFeatures" "perCellQCMetrics" [21] "perFeatureQCMetrics" "pooledSizeFactors" [23] "sumCountsAcrossCells" "sumCountsAcrossFeatures" [25] "summarizeAssayByGroup" Package seriation: [1] "seriate_best" "seriate_rep" Package shapr: [1] "explain" "explain_forecast" Package stats: [1] "kernapply" Package strucchange: [1] "breakpoints.formula" Package sva: [1] "ComBat" "read.degradation.matrix" Package tm: [1] "TermDocumentMatrix" "tm_index" "tm_map" Package vegan: [1] "adonis" "adonis2" "anosim" [4] "anova.cca" "bioenv.default" "cascadeKM" [7] "estaccumR" "mantel" "mantel.partial" [10] "metaMDSiter" "mrpp" "oecosimu" [13] "ordiareatest" "permutest.betadisper" "permutest.cca" Package BiocParallel: [1] ".bpiterate_impl" ".bplapply_impl" ".manager" "bpaggregate" [5] "bpiterate" "bplapply" "bploop.iterate" "bploop.lapply" [9] "bpmapply" "bpvec" Package DESeq2: [1] "DESeq" "lfcShrink" "results" Package GSVA: [1] "gsvaRanks" "gsvaScores" "spatCor" Package GenomicAlignments: [1] "summarizeOverlaps" Package Rsamtools: [1] "countBam" "scanBam" Package SimDesign: [1] "SimSolve" "runArraySimulation" "runSimulation" Package SingleCellExperiment: [1] "applySCE" Package TSP: [1] "solve_TSP" Package base: [1] ".mapply" "Filter" "Map" "apply" "by" "eapply" [7] "lapply" "mapply" "replicate" "sapply" "tapply" "vapply" Package boot: [1] "boot" "censboot" "tsboot" Package caret: [1] "bag" "gafs" "nearZeroVar" "rfe" "safs" [6] "sbf" "train" Package crossmap: [1] "imap_vec" "map2_vec" "map_vec" "pmap_vec" "xmap" "xmap_arr" [7] "xmap_chr" "xmap_dbl" "xmap_dfc" "xmap_dfr" "xmap_int" "xmap_lgl" [13] "xmap_mat" "xmap_raw" "xmap_vec" "xwalk" Package fgsea: [1] "collapsePathwaysGeseca" "fgsea" "fgseaLabel" [4] "fgseaMultilevel" "fgseaSimple" "geseca" [7] "gesecaSimple" Package foreach: [1] "%do%" "%dopar%" Package fwb: [1] "fwb" "vcovFWB" Package gamlss: [1] "add1All" "add1TGD" "addterm.gamlss" "drop1All" [5] "drop1TGD" "dropterm.gamlss" "gamlssCV" Package glmmTMB: [1] "profile.glmmTMB" Package glmnet: [1] "cv.glmnet" Package kernelshap: [1] "kernelshap" "permshap" Package lme4: [1] "allFit" "bootMer" "influence.merMod" "profile.merMod" Package metafor: [1] "cooks.distance.rma.mv" "dfbetas.rma.mv" [3] "gosh.rma" "profile.rma.ls" [5] "profile.rma.mv" "profile.rma.uni" [7] "profile.rma.uni.selmodel" "rstudent.rma.mv" [9] "vif.rma" Package mgcv: [1] "bam" "predict.bam" Package partykit: [1] "cforest" "ctree_control" "mob_control" "varimp.cforest" Package pbapply: [1] "pbapply" "pbby" "pbby.data.frame" "pbby.default" [5] "pbeapply" "pblapply" "pbreplicate" "pbsapply" [9] "pbtapply" "pbvapply" "pbwalk" Package plyr: [1] "a_ply" "aaply" "adply" "alply" "d_ply" "daply" "ddply" "dlply" "l_ply" [10] "laply" "ldply" "llply" "m_ply" "maply" "mdply" "mlply" Package purrr: [1] "imap" "imap_chr" "imap_dbl" "imap_dfc" [5] "imap_dfr" "imap_int" "imap_lgl" "imap_raw" [9] "invoke_map" "invoke_map_chr" "invoke_map_dbl" "invoke_map_dfc" [13] "invoke_map_dfr" "invoke_map_int" "invoke_map_lgl" "invoke_map_raw" [17] "iwalk" "map" "map2" "map2_chr" [21] "map2_dbl" "map2_dfc" "map2_dfr" "map2_int" [25] "map2_lgl" "map2_raw" "map_at" "map_chr" [29] "map_dbl" "map_dfc" "map_dfr" "map_if" [33] "map_int" "map_lgl" "map_raw" "modify" [37] "modify_at" "modify_if" "pmap" "pmap_chr" [41] "pmap_dbl" "pmap_dfc" "pmap_dfr" "pmap_int" [45] "pmap_lgl" "pmap_raw" "pwalk" "walk" [49] "walk2" Package riskRegression: [1] "Score.list" Package scater: [1] "calculatePCA" "calculateTSNE" "calculateUMAP" [4] "getVarianceExplained" "nexprs" "plotRLE" [7] "runColDataPCA" "runTSNE" "runUMAP" Package scuttle: [1] "addPerCellQC" "addPerCellQCMetrics" [3] "addPerFeatureQC" "addPerFeatureQCMetrics" [5] "aggregateAcrossCells" "aggregateAcrossFeatures" [7] "calculateAverage" "computeGeometricFactors" [9] "computeLibraryFactors" "computeMedianFactors" [11] "computePooledFactors" "fitLinearModel" [13] "geometricSizeFactors" "librarySizeFactors" [15] "logNormCounts" "medianSizeFactors" [17] "normalizeCounts" "numDetectedAcrossCells" [19] "numDetectedAcrossFeatures" "perCellQCMetrics" [21] "perFeatureQCMetrics" "pooledSizeFactors" [23] "sumCountsAcrossCells" "sumCountsAcrossFeatures" [25] "summarizeAssayByGroup" Package seriation: [1] "seriate_best" "seriate_rep" Package shapr: [1] "explain" "explain_forecast" Package stats: [1] "kernapply" Package strucchange: [1] "breakpoints.formula" Package sva: [1] "ComBat" "read.degradation.matrix" Package tm: [1] "TermDocumentMatrix" "tm_index" "tm_map" Package vegan: [1] "adonis" "adonis2" "anosim" [4] "anova.cca" "bioenv.default" "cascadeKM" [7] "estaccumR" "mantel" "mantel.partial" [10] "metaMDSiter" "mrpp" "oecosimu" [13] "ordiareatest" "permutest.betadisper" "permutest.cca" Failed to undo environment variables: - Expected environment variables: [n=218] '!ExitCode', 'ALLUSERSPROFILE', 'APPDATA', 'BIBINPUTS', 'BINDIR', 'BSTINPUTS', 'COMMONPROGRAMFILES', 'COMPUTERNAME', 'COMSPEC', 'CURL_CA_BUNDLE', 'CV_Instance001', 'CYGWIN', 'CommonProgramFiles(x86)', 'CommonProgramW6432', 'DriverData', 'HOME', 'HOMEDRIVE', 'HOMEPATH', 'JAGS_ROOT', 'JAVA_HOME', 'LANGUAGE', 'LC_COLLATE', 'LC_MONETARY', 'LC_TIME', 'LOCALAPPDATA', 'LOGONSERVER', 'LS_HOME', 'LS_LICENSE_PATH', 'MAKE', 'MAKEFLAGS', 'MAKELEVEL', 'MFLAGS', 'MSMPI_BENCHMARKS', 'MSMPI_BIN', 'MSYS2_ENV_CONV_EXCL', 'NUMBER_OF_PROCESSORS', 'OCL', 'OMP_THREAD_LIMIT', 'OS', 'PATH', 'PATHEXT', 'PROCESSOR_ARCHITECTURE', 'PROCESSOR_IDENTIFIER', 'PROCESSOR_LEVEL', 'PROCESSOR_REVISION', 'PROGRAMFILES', 'PROMPT', 'PSModulePath', 'PUBLIC', 'PWD', 'ProgramData', 'ProgramFiles(x86)', 'ProgramW6432', 'RTOOLS44_HOME', 'RTOOLS45_HOME', 'R_ARCH', 'R_BROWSER', 'R_BZIPCMD', 'R_CMD', 'R_COMPILED_BY', 'R_CRAN_WEB', 'R_CUSTOM_TOOLS_PATH', 'R_CUSTOM_TOOLS_SOFT', 'R_DOC_DIR', 'R_ENVIRON_USER', 'R_GSCMD', 'R_GZIPCMD', 'R_HOME', 'R_INCLUDE_DIR', 'R_INSTALL_TAR', 'R_LIBS', 'R_LIBS_SITE', 'R_LIBS_USER', 'R_MAX_NUM_DLLS', 'R_OSTYPE', 'R_PAPERSIZE', 'R_PAPERSIZE_USER', 'R_PARALLELLY_MAKENODEPSOCK_AUTOKILL', 'R_PARALLELLY_MAKENODEPSOCK_CONNECTTIMEOUT', 'R_PARALLELLY_MAKENODEPSOCK_RSCRIPT_LABEL', 'R_PARALLELLY_MAKENODEPSOCK_SESSIONINFO_PKGS', 'R_PARALLELLY_MAKENODEPSOCK_TIMEOUT', 'R_PARALLELLY_RANDOM_PORTS', 'R_PARALLEL_PORT', 'R_RD4PDF', 'R_RTOOLS45_PATH', 'R_SCRIPT_LEGACY', 'R_SHARE_DIR', 'R_TESTME_NAME', 'R_TESTME_PACKAGE', 'R_TESTME_PATH', 'R_TESTS', 'R_UNZIPCMD', 'R_USER', 'R_VERSION', 'R_ZIPCMD', 'SED', 'SHLVL', 'SYSTEMDRIVE', 'SYSTEMROOT', 'TAR', 'TAR_OPTIONS', 'TEMP', 'TERM', 'TETRAD_DIR', 'TEXINPUTS', 'TMP', 'TMPDIR', 'USERDOMAIN', 'USERDOMAIN_ROAMINGPROFILE', 'USERNAME', 'USERPROFILE', 'WINDIR', '_', '_R_CHECK_AUTOCONF_', '_R_CHECK_BOGUS_RETURN_', '_R_CHECK_BROWSER_NONINTERACTIVE_', '_R_CHECK_BUILD_VIGNETTES_SEPARATELY_', '_R_CHECK_CODETOOLS_PROFILE_', '_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_', '_R_CHECK_CODE_ATTACH_', '_R_CHECK_CODE_CLASS_IS_STRING_', '_R_CHECK_CODE_DATA_INTO_GLOBALENV_', '_R_CHECK_CODE_USAGE_VIA_NAMESPACES_', '_R_CHECK_CODE_USAGE_WITHOUT_LOADING_', '_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_', '_R_CHECK_CODOC_VARIABLES_IN_USAGES_', '_R_CHECK_COMPACT_DATA2_', '_R_CHECK_COMPILATION_FLAGS_', '_R_CHECK_CONNECTIONS_LEFT_OPEN_', '_R_CHECK_CRAN_INCOMING_', '_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_', '_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_START_', '_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_', '_R_CHECK_CRAN_INCOMING_CHECK_URLS_IN_PARALLEL_', '_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_', '_R_CHECK_CRAN_INCOMING_REMOTE_', '_R_CHECK_CRAN_INCOMING_USE_ASPELL_', '_R_CHECK_DATALIST_', '_R_CHECK_DEPRECATED_DEFUNCT_', '_R_CHECK_DOC_SIZES2_', '_R_CHECK_DOT_FIRSTLIB_', '_R_CHECK_DOT_INTERNAL_', '_R_CHECK_EXAMPLE_TIMING_THRESHOLD_', '_R_CHECK_EXECUTABLES_', '_R_CHECK_EXECUTABLES_EXCLUSIONS_', '_R_CHECK_FF_CALLS_', '_R_CHECK_FF_DUP_', '_R_CHECK_FORCE_SUGGESTS_', '_R_CHECK_FUTURE_FILE_TIMESTAMPS_', '_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_', '_R_CHECK_HAVE_MYSQL_', '_R_CHECK_HAVE_ODBC_', '_R_CHECK_HAVE_PERL_', '_R_CHECK_HAVE_POSTGRES_', '_R_CHECK_INSTALL_DEPENDS_', '_R_CHECK_INTERNALS2_', '_R_CHECK_LENGTH_1_CONDITION_', '_R_CHECK_LICENSE_', '_R_CHECK_LIMIT_CORES_', '_R_CHECK_LOG_USE_INFO_', '_R_CHECK_MATRIX_DATA_', '_R_CHECK_MBCS_CONVERSION_FAILURE_', '_R_CHECK_NATIVE_ROUTINE_REGISTRATION_', '_R_CHECK_NEWS_IN_PLAIN_TEXT_', '_R_CHECK_NO_RECOMMENDED_', '_R_CHECK_NO_STOP_ON_TEST_ERROR_', '_R_CHECK_ORPHANED_', '_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_', '_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_', '_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_', '_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_', '_R_CHECK_PACKAGE_NAME_', '_R_CHECK_PKG_SIZES_', '_R_CHECK_PKG_SIZES_THRESHOLD_', '_R_CHECK_PRAGMAS_', '_R_CHECK_RCPP_NOT_NEEDED_', '_R_CHECK_RD_BIBENTRIES_CITED_NOT_SHOWN_', '_R_CHECK_RD_EXAMPLES_T_AND_F_', '_R_CHECK_RD_LINE_WIDTHS_', '_R_CHECK_RD_MATH_RENDERING_', '_R_CHECK_RD_NOTE_LOST_BRACES_', '_R_CHECK_RD_VALIDATE_RD2HTML_', '_R_CHECK_REPLACING_IMPORTS_', '_R_CHECK_R_DEPENDS_', '_R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_', '_R_CHECK_SCREEN_DEVICE_', '_R_CHECK_SERIALIZATION_', '_R_CHECK_SHLIB_OPENMP_FLAGS_', '_R_CHECK_SRC_MINUS_W_IMPLICIT_', '_R_CHECK_SUBDIRS_NOCASE_', '_R_CHECK_SUGGESTS_ONLY_', '_R_CHECK_SYSTEM_CLOCK_', '_R_CHECK_TESTS_NLINES_', '_R_CHECK_TEST_TIMING_', '_R_CHECK_TIMINGS_', '_R_CHECK_TOPLEVEL_FILES_', '_R_CHECK_UNDOC_USE_ALL_NAMES_', '_R_CHECK_UNSAFE_CALLS_', '_R_CHECK_URLS_RELATIVE_PATHS_', '_R_CHECK_URLS_SHOW_301_STATUS_', '_R_CHECK_VC_DIRS_', '_R_CHECK_VIGNETTES_NLINES_', '_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_', '_R_CHECK_VIGNETTE_TIMING_', '_R_CHECK_VIGNETTE_TITLES_', '_R_CHECK_WINDOWS_DEVICE_', '_R_CHECK_XREFS_NOTE_MISSING_PACKAGE_ANCHORS_', '_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_', '_R_CLASS_MATRIX_ARRAY_', '_R_DEPRECATED_IS_R_', '_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_', '_R_USE_STRICT_R_HEADERS_', '__R_CHECK_DOC_FILES_NOTE_IF_ALL_INTERNAL__', 'maj.version', 'nextArg--timingsnextArg--install', 'tempdirname' - Environment variables still there: [n=0] - Environment variables missing: [n=1] 'MAKEFLAGS' Differences environment variable by environment variable: Skipping, because path appears not to be an 'R CMD check' folder: 'D:/temp/2026_03_18_16_10_17_7961' Test time: user.self=2e+01s, sys.self=3s, elapsed=3e+01s, user.child=NAs, sys.child=NAs Test 'api' ... success > > proc.time() user system elapsed 24.56 3.40 27.21