Package Install Failing

[samuel-marsh]

Hi,

Getting an error trying to install miQC when build_vignettes = TRUE due to what seems to be an error downloading datasets. Installation proceeds fine when set to FALSE. Error and sessionInfo below:

E  creating vignettes (21.8s)
   --- re-building ‘miQC.Rmd’ using rmarkdown
   snapshotDate(): 2021-05-18
   see ?scRNAseq and browseVignettes('scRNAseq') for documentation
   downloading 1 resources
   retrieving 1 resource
   Warning: download failed
     web resource path: 'https://experimenthub.bioconductor.org/fetch/2596'
     local file path: '/Users/marsh_imac/Library/Caches/org.R-project.R/R/ExperimentHub/91f67e535f4a_2596'
     reason: Not Found (HTTP 404).
   Warning: bfcadd() failed; resource removed
     rid: BFC4
     fpath: 'https://experimenthub.bioconductor.org/fetch/2596'
     reason: download failed
   Warning: download failed
     hub path: 'https://experimenthub.bioconductor.org/fetch/2596'
     cache resource: 'EH2580 : 2596'
     reason: bfcadd() failed; see warnings()
   Quitting from lines 70-72 (miQC.Rmd) 
   Error: processing vignette 'miQC.Rmd' failed with diagnostics:
   failed to load resource
     name: EH2580
     title: Zeisel brain counts
     reason: 1 resources failed to download
   --- failed re-building ‘miQC.Rmd’
   
   SUMMARY: processing the following file failed:
     ‘miQC.Rmd’
   
   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'miQC' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E>   name: EH2580
E>   title: Zeisel brain counts
E>   reason: 1 resources failed to download
E> --- failed re-building ‘miQC.Rmd’
E> 
E> SUMMARY: processing the following file failed:
E>   ‘miQC.Rmd’
E> 
E> Error: Vignette re-building failed.
E> Execution halted

sessionInfo

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7          rstudioapi_0.13     magrittr_2.0.1      usethis_2.0.1       devtools_2.4.2      pkgload_1.2.1      
 [7] R6_2.5.0            rlang_0.4.11        fastmap_1.1.0       sys_3.4             tools_4.1.0         pkgbuild_1.2.0     
[13] sessioninfo_1.1.1   cli_3.0.1           withr_2.4.2         askpass_1.1         ellipsis_0.3.2      remotes_2.4.0      
[19] openssl_1.4.4       rprojroot_2.0.2     lifecycle_1.0.0     crayon_1.4.1        processx_3.5.2      purrr_0.3.4        
[25] BiocManager_1.30.16 callr_3.7.0         credentials_1.3.1   fs_1.5.0            ps_1.6.0            testthat_3.0.4     
[31] curl_4.3.2          glue_1.4.2          memoise_2.0.0       cachem_1.0.5        compiler_4.1.0      desc_1.3.0         
[37] prettyunits_1.1.1   jsonlite_1.7.2

[carlosaya2]

Hi,

I am having the same issue. any issues when running on false?

Thank you

[arielah]

It could be an issue with the EnsemblDB site or one of its mirrors being down. Are you still experiencing the same issue now?