This page was generated on 2024-03-28 11:39:38 -0400 (Thu, 28 Mar 2024).
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSstatsPTM
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* 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 ...