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This page was generated on 2024-03-28 11:39:38 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R 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 1347/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.5.4  (landing page)
Devon Kohler
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: devel
git_last_commit: c8e6285
git_last_commit_date: 2024-02-13 09:03:34 -0400 (Tue, 13 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for MSstatsPTM on lconway


To the developers/maintainers of the MSstatsPTM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.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.

raw results


Summary

Package: MSstatsPTM
Version: 2.5.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsPTM
StartedAt: 2024-03-27 17:30:52 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 17:31:50 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 58.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsPTM
###
##############################################################################
##############################################################################


* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* preparing ‘MSstatsPTM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 16315 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmpr6QGUP/xshell346a702dc410' 2>&1
 ERROR
--- re-building ‘MSstatsPTM_LabelFree_Workflow.Rmd’ using rmarkdown
2024-03-27 17:31:46.492 R[16315:1358643281] XType: com.apple.fonts is not accessible.
2024-03-27 17:31:46.492 R[16315:1358643281] XType: XTFontStaticRegistry is enabled.

 *** caught segfault ***
address 0x0, 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$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 8L, 0L, 8L, 1L, 9L, 1L, 9L, 2L, 8L, 2L, 8L, 3L, 9L, 3L, 9L, 4L, 8L, 4L, 8L, 5L, 9L, 5L, 9L, 6L, 8L, 6L, 8L, 7L, 9L, 7L, 9L), p = c(0L, 2L, 4L, 6L, 8L, 10L, 12L, 14L, 16L, 18L, 20L, 22L, 24L, 26L, 28L, 30L, 32L), Dim = c(10L, 16L), Dimnames = list(c("CCCP:BCH1", "CCCP:BCH2", "Combo:BCH1", "Combo:BCH2", "Ctrl:BCH1", "Ctrl:BCH2", "USP30_OE:BCH1", "USP30_OE:BCH2", "BCH1", "BCH2"), c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()),     theta = c(1, 1), Lambdat = new("dgCMatrix", i = 0:9, p = 0:10,         Dim = c(10L, 10L), Dimnames = list(NULL, NULL), x = c(1,         1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), Lind = c(1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L), n = 16L, X = c(1, 1,     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1,     1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,     1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,     0, 1, 1, 1, 1))
 8: do.call(merPredD$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(ABUNDANCE = c(19.1938546296373, 19.9078684924615, 21.8112981828596, 21.7128565299469, 19.9057402192649, 19.1908991238328, 21.7375048468547, 22.0381612260309, 19.648522128431, 20.5454621079787, 21.7114836559556, 21.7957696042591, 20.6905489667604, 20.8798960863835, 22.0157230127491, 21.6502232477305), GROUP = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L), SUBJECT = c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L)),     X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,     0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,     0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,     0, 0, 0, 0, 0, 1, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix",         i = c(0L, 8L, 0L, 8L, 1L, 9L, 1L, 9L, 2L, 8L, 2L, 8L,         3L, 9L, 3L, 9L, 4L, 8L, 4L, 8L, 5L, 9L, 5L, 9L, 6L, 8L,         6L, 8L, 7L, 9L, 7L, 9L), p = c(0L, 2L, 4L, 6L, 8L, 10L,         12L, 14L, 16L, 18L, 20L, 22L, 24L, 26L, 28L, 30L, 32L        ), Dim = c(10L, 16L), Dimnames = list(c("CCCP:BCH1",         "CCCP:BCH2", "Combo:BCH1", "Combo:BCH2", "Ctrl:BCH1",         "Ctrl:BCH2", "USP30_OE:BCH1", "USP30_OE:BCH2", "BCH1",         "BCH2"), c("1", "2", "3", "4", "5", "6", "7", "8", "9",         "10", "11", "12", "13", "14", "15", "16")), x = c(1,         1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,         1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()),         theta = c(1, 1), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,         1L, 2L, 2L), Gp = c(0L, 8L, 10L), lower = c(0, 0), Lambdat = new("dgCMatrix",             i = 0:9, p = 0:10, Dim = c(10L, 10L), Dimnames = list(                NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1,             1), factors = list()), flist = list(`GROUP:SUBJECT` = c(1L,         1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L,         8L), SUBJECT = c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,         1L, 2L, 2L, 1L, 1L, 2L, 2L)), cnms = list(`GROUP:SUBJECT` = "(Intercept)",             SUBJECT = "(Intercept)"), Ztlist = list(`1 | GROUP:SUBJECT` = new("dgCMatrix",             i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L,             5L, 6L, 6L, 7L, 7L), p = 0:16, Dim = c(8L, 16L),             Dimnames = list(c("CCCP:BCH1", "CCCP:BCH2", "Combo:BCH1",             "Combo:BCH2", "Ctrl:BCH1", "Ctrl:BCH2", "USP30_OE:BCH1",             "USP30_OE:BCH2"), c("1", "2", "3", "4", "5", "6",             "7", "8", "9", "10", "11", "12", "13", "14", "15",             "16")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,             1, 1, 1, 1), factors = list()), `1 | SUBJECT` = new("dgCMatrix",             i = c(0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,             1L, 0L, 0L, 1L, 1L), p = 0:16, Dim = c(2L, 16L),             Dimnames = list(c("BCH1", "BCH2"), c("1", "2", "3",             "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",             "14", "15", "16")), x = c(1, 1, 1, 1, 1, 1, 1, 1,             1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(`GROUP:SUBJECT` = 8L,         SUBJECT = 2L)), 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: lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT) + (1 | GROUP:SUBJECT),     data = input)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
16: try(lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT) + (1 | GROUP:SUBJECT),     data = input), TRUE)
17: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
18: suppressMessages(try(lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT) +     (1 | GROUP:SUBJECT), data = input), TRUE))
19: .fitModelForGroupComparison(input, repeated, is_single_subject,     has_tech_replicates)
20: .fitModelSingleProtein(single_protein, contrast_matrix, has_tech_reps,     is_single_subject, repeated, groups, samples_info, save_fitted_models,     has_imputed)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
25: try(.fitModelSingleProtein(single_protein, contrast_matrix, has_tech_reps,     is_single_subject, repeated, groups, samples_info, save_fitted_models,     has_imputed), silent = TRUE)
26: MSstatsGroupComparisonSingleProtein(summarized_list[[i]], contrast_matrix,     repeated, groups, samples_info, save_fitted_models, has_imputed)
27: MSstatsGroupComparison(split_summarized, contrast_matrix, save_fitted_models,     repeated, samples_info)
28: groupComparison(contrast.matrix, data.ptm, TRUE, log_base, use_log_file,     append, verbose, log_file_path = path)
29: groupComparisonPTM(MSstatsPTM.summary, data.type = "LabelFree",     contrast.matrix = comparison, use_log_file = FALSE, append = FALSE,     verbose = FALSE)
30: eval(expr, envir, enclos)
31: eval(expr, envir, enclos)
32: eval_with_user_handlers(expr, envir, enclos, user_handlers)
33: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
34: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
35: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
36: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
37: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group.block(group)
46: process_group(group)
47: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
48: withCallingHandlers(expr, error = function(e) {    loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile")))    message(one_string(handler(e, loc)))})
49: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(e, loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
50: process_file(text, output)
51: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
53: vweave_rmarkdown(...)
54: engine$weave(file, quiet = quiet, encoding = enc)
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
59: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...