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This page was generated on 2023-02-08 01:15:06 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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BUILD results for GeomxTools on kunpeng1


To the developers/maintainers of the GeomxTools package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 791/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeomxTools 3.3.0  (landing page)
Nicole Ortogero
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/GeomxTools
git_branch: master
git_last_commit: 9bd00a9
git_last_commit_date: 2022-11-01 15:23:52 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    ERROR  skipped

Summary

Package: GeomxTools
Version: 3.3.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools
StartedAt: 2023-02-06 08:42:11 -0000 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 08:51:23 -0000 (Mon, 06 Feb 2023)
EllapsedTime: 551.8 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 313-314 (GeomxSet_coercions.Rmd) 
Error: processing vignette 'GeomxSet_coercions.Rmd' failed with diagnostics:
there is no package called 'SpatialExperiment'
--- failed 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:
  ‘GeomxSet_coercions.Rmd’

Error: Vignette re-building failed.
Execution halted