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

Quitting from musmusculus.Rmd:41-67 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getUrl()`:
! Bad Request (HTTP 400).
---
Backtrace:
    x
 1. \-FELLA::buildGraphFromKEGGREST(...)
 2.   \-plyr::alply(...)
 3.     \-plyr::llply(...)
 4.       +-plyr:::loop_apply(n, do.ply)
 5.       \-plyr (local) `<fn>`(1L)
 6.         \-FELLA (local) .fun(piece, ...)
 7.           \-KEGGREST::keggLink(row[1], row[2])
 8.             \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 9.               \-httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
Bad Request (HTTP 400).
--- failed re-building ‘musmusculus.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
2025-03-31 23:29:40.235 R[69942:338705794] XType: Using static font registry.
--- finished re-building ‘quickstart.Rmd’

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

Quitting from zebrafish.Rmd:50-74 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getUrl()`:
! Bad Request (HTTP 400).
---
Backtrace:
    x
 1. \-FELLA::buildGraphFromKEGGREST(organism = "dre", filter.path = c("01100"))
 2.   \-plyr::alply(...)
 3.     \-plyr::llply(...)
 4.       +-plyr:::loop_apply(n, do.ply)
 5.       \-plyr (local) `<fn>`(1L)
 6.         \-FELLA (local) .fun(piece, ...)
 7.           \-KEGGREST::keggLink(row[1], row[2])
 8.             \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 9.               \-httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
Bad Request (HTTP 400).
--- failed re-building ‘zebrafish.Rmd’

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 2 (label = 01_graph) 
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).

--- failed re-building ‘FELLA.Rnw’

SUMMARY: processing the following files failed:
  ‘musmusculus.Rmd’ ‘zebrafish.Rmd’ ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted