This page was generated on 2024-04-17 11:37:46 -0400 (Wed, 17 Apr 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 GeomxTools
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* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* preparing ‘GeomxTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 43758 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpbTcY66/xshell9b33d7f4b2c' 2>&1
ERROR
--- re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using rmarkdown
--- finished re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’
--- re-building ‘GeomxSet_coercions.Rmd’ using rmarkdown
2024-04-15 19:07:02.233 R[43758:2530175542] XType: com.apple.fonts is not accessible.
2024-04-15 19:07:02.234 R[43758:2530175542] XType: XTFontStaticRegistry is enabled.
Calculating gene variances
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Calculating feature variances of standardized and clipped values
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|======================================================================| 100%
Using method 'umap'
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**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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| | 0%
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|=================================== | 50%
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|======================================================================| 100%
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
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--- finished re-building ‘GeomxSet_coercions.Rmd’
--- re-building ‘Protein_in_GeomxTools.Rmd’ using rmarkdown
*** caught segfault ***
address 0x0, cause 'unknown'
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Traceback:
1: xpdrows.data.frame(x, rows, new.rows)
2: `[<-.data.frame`(`*tmp*`, nrow(lookup_df) + 1, , value = list( "RTS0052099", "MARCHF7", "Hs_R_NGS_WTA_v1.0", "Endogenous", "51987", "64844", "MARCHF7"))
3: `[<-`(`*tmp*`, nrow(lookup_df) + 1, , value = list("RTS0052099", "MARCHF7", "Hs_R_NGS_WTA_v1.0", "Endogenous", "51987", "64844", "MARCHF7"))
4: generate_pkc_lookup(jsons_vec = pkc_json_list)
5: readPKCFile(pkcFiles, default_pkc_vers = defaultPKCVersions)
6: readNanoStringGeoMxSet(dccFiles = DCCFiles, pkcFiles = PKCFiles, phenoDataFile = SampleAnnotationFile, phenoDataSheet = "Annotations", phenoDataDccColName = "Sample_ID", protocolDataColNames = c("Tissue", "Segment_Type", "ROI.Size"), configFile = NULL, analyte = "RNA", phenoDataColPrefix = "", experimentDataColNames = NULL)
7: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
8: suppressWarnings(readNanoStringGeoMxSet(dccFiles = DCCFiles, pkcFiles = PKCFiles, phenoDataFile = SampleAnnotationFile, phenoDataSheet = "Annotations", phenoDataDccColName = "Sample_ID", protocolDataColNames = c("Tissue", "Segment_Type", "ROI.Size"), configFile = NULL, analyte = "RNA", phenoDataColPrefix = "", experimentDataColNames = NULL))
9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: eval_with_user_handlers(expr, envir, enclos, user_handlers)
12: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
13: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
14: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
17: evaluate::evaluate(...)
18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
19: in_dir(input_dir(), expr)
20: 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$render, options)))
21: eng_r(options)
22: block_exec(params)
23: call_block(x)
24: process_group(group)
25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
26: withCallingHandlers(expr, error = function(e) { loc = if (is.function(fun)) trimws(fun(label)) else "" if (loc != "") loc = sprintf(" at lines %s", loc) message(one_string(handler(e, loc)))})
27: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: 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)))})
37: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...