Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:21 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 488/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CyTOFpower 1.9.0 (landing page) Anne-Maud Ferreira
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the CyTOFpower package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CyTOFpower.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: CyTOFpower |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CyTOFpower_1.9.0.tar.gz |
StartedAt: 2024-03-27 21:36:28 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:37:28 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 60.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: CyTOFpower.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CyTOFpower_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CyTOFpower.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘CyTOFpower/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CyTOFpower’ version ‘1.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CyTOFpower’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Changes in version 0.99.0 (2021-09-15) * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 40: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 41: source_file(path, env = env(env), desc = desc, error_call = error_call) 42: FUN(X[[i]], ...) 43: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 44: doTryCatch(return(expr), name, parentenv, handler) 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 46: tryCatchList(expr, classes, parentenv, handlers) 47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 52: test_check("CyTOFpower") An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped) * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/CyTOFpower.Rcheck/00check.log’ for details.
CyTOFpower.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CyTOFpower ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘CyTOFpower’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CyTOFpower)
CyTOFpower.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > library(testthat) > library(CyTOFpower) > > test_check("CyTOFpower") [[1]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1 0.1 10 3 1 [[2]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m2 3 1.1 0.1 10 3 1 marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1.0 0.1 10 3 3 2 m2 3 1.1 0.1 10 3 3 3 m3 3 1.0 0.1 10 3 3 marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1.0 0.1 10 3 3 2 m2 3 1.1 0.1 10 3 3 3 m3 3 1.0 0.1 10 3 3 marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1.0 0.1 10 3 3 2 m2 3 1.1 0.1 10 3 3 3 m3 3 1.0 0.1 10 3 3 [[1]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1 0.1 10 3 3 [[2]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m2 3 1.1 0.1 10 3 3 [[3]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m3 3 1 0.1 10 3 3 [[1]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1 0.1 10 3 3 [[2]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m2 3 1.1 0.1 10 3 3 [[3]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m3 3 1 0.1 10 3 3 [[1]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m1 3 1 0.1 10 3 3 [[2]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m2 3 1.1 0.1 10 3 3 [[3]] marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample 1 m3 3 1 0.1 10 3 3 Joining with `by = join_by(markers)` Joining with `by = join_by(markers)` *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6, Dim = c(3L, 6L), Dimnames = list(c("donor_1", "donor_2", "donor_3"), c("sample_1", "sample_4", "sample_2", "sample_5", "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L), n = 6L, X = c(1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(y = c(1.5296604950904, 0.732668256045411, 1.35044074027497, 1.35044074027497, 1.75322890111027, 1.35044074027497), group_id = c(1L, 2L, 1L, 2L, 1L, 2L), donor_id = c(1L, 1L, 2L, 2L, 3L, 3L), `(weights)` = c(3, 3, 3, 3, 3, 3)), X = c(1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1), reTrms = list( Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6, Dim = c(3L, 6L), Dimnames = list(c("donor_1", "donor_2", "donor_3"), c("sample_1", "sample_4", "sample_2", "sample_5", "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L, 1L), Gp = c(0L, 3L), lower = 0, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), flist = list(donor_id = c(1L, 1L, 2L, 2L, 3L, 3L)), cnms = list( donor_id = "(Intercept)"), Ztlist = list(`1 | donor_id` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L), p = 0:6, Dim = c(3L, 6L ), Dimnames = list(c("donor_1", "donor_2", "donor_3"), c("sample_1", "sample_4", "sample_2", "sample_5", "sample_3", "sample_6")), x = c(1, 1, 1, 1, 1, 1), factors = list())), nl = c(donor_id = 3L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list( optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list( check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lmer(formula$formula, data = data_i, weights = weights) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: tryCatch({ y <- meds[i, ] data_i <- cbind(cbind(y, weights), formula$data) if (formula$random_terms) { fit <- lmer(formula$formula, data = data_i, weights = weights) } else { fit <- lm(formula$formula, data = data_i, weights = weights) } test <- glht(fit, contrast) summary(test)$test$pvalues}, error = function(e) NA) 16: diffcyt::testDS_LMM(d_counts = ls_features$counts, d_medians = ls_features$medians, formula = ls_form_contrast$formula, contrast = ls_form_contrast$contrast) 17: function_run_diffcytDSLMM(ls_form_contrast = ls_contrast_LMM, df_experiment_info = df_exp_info, ls_features = ls_features) 18: eval(code, test_env) 19: eval(code, test_env) 20: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 21: doTryCatch(return(expr), name, parentenv, handler) 22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 24: doTryCatch(return(expr), name, parentenv, handler) 25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 26: tryCatchList(expr, classes, parentenv, handlers) 27: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 28: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 29: test_that("Run diffcyt-DS-LMM model", { set.seed(123) ls_contrast_LMM <- function_formula_contrast_diffcytDSLMM_randomeffect(df_experiment_info = df_exp_info) ls_features <- function_compute_diffcyt_features(d_sumexp) ls_res_model_lmm <- function_run_diffcytDSLMM(ls_form_contrast = ls_contrast_LMM, df_experiment_info = df_exp_info, ls_features = ls_features) expect_type(ls_res_model_lmm, "list") expect_identical(names(ls_res_model_lmm), c("model_fit", "result_summary")) expect_equal(ls_res_model_lmm$result_summary$p_adj, c(0.1, 0, 0.5), tolerance = 1)}) 30: eval(code, test_env) 31: eval(code, test_env) 32: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 33: doTryCatch(return(expr), name, parentenv, handler) 34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 35: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 36: doTryCatch(return(expr), name, parentenv, handler) 37: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 38: tryCatchList(expr, classes, parentenv, handlers) 39: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 40: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 41: source_file(path, env = env(env), desc = desc, error_call = error_call) 42: FUN(X[[i]], ...) 43: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 44: doTryCatch(return(expr), name, parentenv, handler) 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 46: tryCatchList(expr, classes, parentenv, handlers) 47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 52: test_check("CyTOFpower") An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)
CyTOFpower.Rcheck/CyTOFpower-Ex.timings
name | user | system | elapsed | |
CyTOFpower | 0.000 | 0.000 | 0.001 | |