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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gemma.R
###
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* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown

Quitting from gemma.R.Rmd:325-328 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.body()`:
! https://gemma.msl.ubc.ca/rest/v2/resultSets/550248
500: Internal server error.
---
Backtrace:
     ▆
  1. └─gemma.R::get_differential_expression_values("GSE46416")
  2.   └─base::lapply(...)
  3.     └─gemma.R (local) FUN(X[[i]], ...)
  4.       └─gemma.R:::.getResultSets(x, memoised = memoised)
  5.         └─gemma.R:::mem.getResultSets(...)
  6.           ├─gemma.R (local) mem_call(...)
  7.           │ ├─base::withVisible(eval(mc, parent.frame()))
  8.           │ └─base::eval(mc, parent.frame())
  9.           │   └─base::eval(mc, parent.frame())
 10.           └─gemma.R (local) `<fn>`(...)
 11.             └─gemma.R:::.body(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
https://gemma.msl.ubc.ca/rest/v2/resultSets/550248
500: Internal server error.
--- failed re-building ‘gemma.R.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown

Quitting from metadata.Rmd:131-142 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sum()`:
! invalid 'type' (list) of argument
---
Backtrace:
    ▆
 1. └─... %>% sum
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metadata.Rmd' failed with diagnostics:
invalid 'type' (list) of argument
--- failed re-building ‘metadata.Rmd’

--- re-building ‘metanalysis.Rmd’ using rmarkdown

Quitting from metanalysis.Rmd:225-238 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.body()`:
! https://gemma.msl.ubc.ca/rest/v2/resultSets/515364
500: Internal server error.
---
Backtrace:
     ▆
  1. ├─parkin_contrasts$result.ID %>% ...
  2. ├─BiocGenerics::lapply(...)
  3. └─base::lapply(...)
  4.   └─FUN(X[[i]], ...)
  5.     └─gemma.R::get_differential_expression_values(resultSets = x)
  6.       └─base::lapply(...)
  7.         └─gemma.R (local) FUN(X[[i]], ...)
  8.           └─gemma.R:::.getResultSets(x, memoised = memoised)
  9.             └─gemma.R:::mem.getResultSets(...)
 10.               ├─gemma.R (local) mem_call(...)
 11.               │ ├─base::withVisible(eval(mc, parent.frame()))
 12.               │ └─base::eval(mc, parent.frame())
 13.               │   └─base::eval(mc, parent.frame())
 14.               └─gemma.R (local) `<fn>`(...)
 15.                 └─gemma.R:::.body(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
https://gemma.msl.ubc.ca/rest/v2/resultSets/515364
500: Internal server error.
--- failed re-building ‘metanalysis.Rmd’

SUMMARY: processing the following files failed:
  ‘gemma.R.Rmd’ ‘metadata.Rmd’ ‘metanalysis.Rmd’

Error: Vignette re-building failed.
Execution halted