Multiple platform build/check report for BioC 3.21 - BUILD results for GeomxTools on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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*

BUILD results for GeomxTools on lconway

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: 3.12.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools

StartedAt: 2025-04-21 16:56:25 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 17:02:42 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 377.8 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 ... ERROR
--- re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using rmarkdown

Quitting from Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd:197-211 [applyFunctions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `multiassign()`:
! envir argument is not an environment
---
Backtrace:
    ▆
 1. ├─NanoStringNCTools::assayDataApply(...)
 2. └─NanoStringNCTools::assayDataApply(...)
 3.   └─NanoStringNCTools (local) .local(X, MARGIN, FUN, ...)
 4.     └─NanoStringNCTools:::.apply(...)
 5.       └─Biobase::multiassign(names(.kvs), .kvs, environment(FUN))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd' failed with diagnostics:
envir argument is not an environment
--- failed re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’

--- re-building ‘GeomxSet_coercions.Rmd’ using rmarkdown
2025-04-21 16:59:03.678 R[5539:723433302] XType: com.apple.fonts is not accessible.
2025-04-21 16:59:03.679 R[5539:723433302] XType: XTFontStaticRegistry is enabled.
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
--- finished re-building ‘Protein_in_GeomxTools.Rmd’

SUMMARY: processing the following file failed:
  ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’

Error: Vignette re-building failed.
Execution halted