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This page was generated on 2023-10-16 11:35:24 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 823/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.4.0  (landing page)
Nicole Ortogero
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: RELEASE_3_17
git_last_commit: 776a43c
git_last_commit_date: 2023-04-25 11:26:17 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD results for GeomxTools on nebbiolo1


To the developers/maintainers of the GeomxTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeomxTools.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: GeomxTools
Version: 3.4.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools
StartedAt: 2023-10-15 16:55:54 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 16:59:57 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 243.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/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 ... 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
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 0x55d800000004, cause 'memory not mapped'
*** recursive gc invocation
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Traceback:
 1: xpdrows.data.frame(x, rows, new.rows)
 2: `[<-.data.frame`(`*tmp*`, nrow(lookup_df) + 1, , value = list(    "RTS0025482", "UCHL5", "Hs_R_NGS_WTA_v1.0", "Endogenous",     "39774", "51377", "UCHL5"))
 3: `[<-`(`*tmp*`, nrow(lookup_df) + 1, , value = list("RTS0025482",     "UCHL5", "Hs_R_NGS_WTA_v1.0", "Endogenous", "39774", "51377",     "UCHL5"))
 4: generate_pkc_lookup(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$render, options)))
21: eng_r(options)
22: block_exec(params)
23: call_block(x)
24: process_group.block(group)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
27: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
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 ...
Segmentation fault (core dumped)