markrobinsonuzh/cytofWorkflow

Error: package or namespace load failed for ‘HDCytoData’

rohitfarmer opened this issue · 2 comments

rohitfarmer commented

I am trying to install CyTOF Workflow version 4 on R 4.1 and it seems that it's crashing because of HDCytoData. So, I tried to install HDCytoData separately and I am getting the following error. Any suggestion to troubleshoot this would be helpful. Thanks.

* installing *source* package ‘HDCytoData’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
There were 12 warnings (use warnings() to see them)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package ‘ExperimentHub’ was built under R version 4.1.2
Warning: package ‘BiocGenerics’ was built under R version 4.1.1
Warning: package ‘AnnotationHub’ was built under R version 4.1.2
Warning: package ‘BiocFileCache’ was built under R version 4.1.2
Warning: package ‘SummarizedExperiment’ was built under R version 4.1.1
Warning: package ‘MatrixGenerics’ was built under R version 4.1.1
Warning: package ‘GenomicRanges’ was built under R version 4.1.2
Warning: package ‘S4Vectors’ was built under R version 4.1.2
Warning: package ‘IRanges’ was built under R version 4.1.1
Warning: package ‘GenomeInfoDb’ was built under R version 4.1.2
Warning: package ‘Biobase’ was built under R version 4.1.1
Warning: package ‘flowCore’ was built under R version 4.1.1
Error: package or namespace load failed for ‘HDCytoData’:
 .onLoad failed in loadNamespace() for 'HDCytoData', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'query': DEFUNCT: As of ExperimentHub (>1.17.2), default caching location has changed.
  Problematic cache: /Users/farmerr2/Library/Caches/ExperimentHub
  See https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html#default-caching-location-update

Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/farmerr2/Library/R/x86_64/4.1/library/HDCytoData’

The downloaded source packages are in
	‘/private/var/folders/65/jmp3d3y56yx2tcl19zf4g6mwrp6krd/T/RtmpaFG4Am/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.1/Resources/library
  packages:
    class, foreign, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Warning message:
In .inet_warning(msg) :
  installation of package ‘HDCytoData’ had non-zero exit status
markrobinsonuzh commented

Hi @rohitfarmer,

I'm not able to reproduce this error on my Mac ..

> BiocManager::install("HDCytoData")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'HDCytoData'
[snip]
* installing *source* package ‘HDCytoData’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-10-19
** testing if installed package can be loaded from final location
snapshotDate(): 2021-10-19
** testing if installed package keeps a record of temporary installation path
* DONE (HDCytoData)

Did you follow the instructions in the noted link: https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html#default-caching-location-update ?

As mentioned there, another option is to delete the cache directory listed.

Hope that helps,
Mark

  • 👍1
rohitfarmer commented

@markrobinsonuzh Clearing cache worked. Everything seems to be installed now. Thank you for your help.

  • 👍1