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This page was generated on 2021-10-15 15:06:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GeneExpressionSignature package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneExpressionSignature.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 712/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneExpressionSignature 1.38.0 (landing page) Yang Cao
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
Package: GeneExpressionSignature |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeneExpressionSignature |
StartedAt: 2021-10-14 12:13:11 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 12:13:19 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 7.7 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeneExpressionSignature ### ############################################################################## ############################################################################## * checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK * preparing ‘GeneExpressionSignature’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ...sh: line 1: 71281 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmph3TtKe/xshell11408774cbecd' 2>&1 ERROR --- re-building ‘GeneExpressionSignature.Rmd’ using rmarkdown Loading required package: GEOquery Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Rows: 33699 Columns: 3 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): ID_REF, VALUE, ABS_CALL ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. *** caught segfault *** address 0x7fc76ffffff8, cause 'memory not mapped' Traceback: 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, col_types = col_types, id = id, skip = skip, col_select = col_select, name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws, escape_double = escape_double, escape_backslash = escape_backslash, comment = comment, skip_empty_rows = skip_empty_rows, locale = locale, guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep), num_threads = num_threads, progress = progress) 2: vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types, col_select = { { col_select } }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max, na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows, trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE, locale = locale, guess_max = guess_max, show_col_types = show_col_types, progress = progress, altrep = lazy, num_threads = num_threads) 3: read_tsv(paste(tbltxt, collapse = "\n"), comment = "!sample_table_end", guess_max = 10000, na = .na_strings) 4: .parseGSMTxt(txt) 5: parseGSM(fname) 6: parseGEO(filename, GSElimits, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL) 7: getGEO(filename = system.file("extdata/GSM118721.soft", package = "GeneExpressionSignature")) 8: eval(expr, envir, enclos) 9: eval(expr, envir, enclos) 10: withVisible(eval(expr, envir, enclos)) 11: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) 12: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) 13: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) 14: evaluate_call(expr, parsed$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, output_handler = output_handler, include_timing = include_timing) 15: evaluate::evaluate(...) 16: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options)) 17: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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))) 18: eng_r(options) 19: block_exec(params) 20: call_block(x) 21: process_group.block(group) 22: process_group(group) 23: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) 24: process_file(text, output) 25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 27: vweave_rmarkdown(...) 28: engine$weave(file, quiet = quiet, encoding = enc) 29: doTryCatch(return(expr), name, parentenv, handler) 30: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 31: tryCatchList(expr, classes, parentenv, handlers) 32: 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)))}) 33: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ...