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This page was generated on 2024-04-18 11:32:11 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 839/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.6.2  (landing page)
Maddy Griswold
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: RELEASE_3_18
git_last_commit: fb59586
git_last_commit_date: 2024-02-09 13:23:59 -0400 (Fri, 09 Feb 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for GeomxTools on kjohnson1


To the developers/maintainers of the GeomxTools package:
- 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: GeomxTools
Version: 3.6.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools
StartedAt: 2024-04-16 18:54:15 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 18:58:32 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 257.3 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 GeomxTools
###
##############################################################################
##############################################################################


* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* preparing ‘GeomxTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1:  5600 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpQ9SmQQ/xshell150f28a188e9' 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
2024-04-16 18:57:50.183 R[5600:449481194] XType: Using static font registry.
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘GeomxSet_coercions.Rmd’

--- re-building ‘Protein_in_GeomxTools.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x100000001, cause 'invalid permissions'
*** recursive gc invocation
*** recursive gc invocation
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Traceback:
 1: duplicated.default(nm)
 2: duplicated(nm)
 3: xpdrows.data.frame(x, rows, new.rows)
 4: `[<-.data.frame`(`*tmp*`, nrow(lookup_df) + 1, , value = list(    "RTS0021560", "HRH1", "Hs_R_NGS_WTA_v1.0", "Endogenous",     "36211", "3269", "HRH1"))
 5: `[<-`(`*tmp*`, nrow(lookup_df) + 1, , value = list("RTS0021560",     "HRH1", "Hs_R_NGS_WTA_v1.0", "Endogenous", "36211", "3269",     "HRH1"))
 6: generate_pkc_lookup(jsons_vec = pkc_json_list)
 7: readPKCFile(pkcFiles, default_pkc_vers = defaultPKCVersions)
 8: 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: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
10: 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))
11: eval(expr, envir, enclos)
12: eval(expr, envir, enclos)
13: eval_with_user_handlers(expr, envir, enclos, user_handlers)
14: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
15: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
16: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
17: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
18: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
19: evaluate::evaluate(...)
20: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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: in_dir(input_dir(), expr)
22: 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$render, options)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group.block(group)
27: process_group(group)
28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
29: withCallingHandlers(expr, error = function(e) {    loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile")))    message(one_string(handler(e, loc)))})
30: 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]))
31: process_file(text, output)
32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
34: vweave_rmarkdown(...)
35: engine$weave(file, quiet = quiet, encoding = enc)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch({    engine$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)))})
40: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...