##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r wppi -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
##############################################################################


* checking for file 'wppi/DESCRIPTION' ... OK
* preparing 'wppi':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'wppi_workflow.Rmd' using rmarkdown
[2021-10-14 19:09:31] [INFO]    [wppi] Executing WPPI workflow.
[2021-10-14 19:09:31] [INFO]    [wppi] Collecting database knowledge.
[2021-10-14 19:09:33] [SUCCESS] [OmnipathR] Human Phenotype Ontology (ci.monarchinitiative.org): loaded 234119 records from cache
[2021-10-14 19:09:39] [SUCCESS] [OmnipathR] Gene Ontology (geneontology.org): loaded 619347 records from cache
[2021-10-14 19:09:41] [SUCCESS] [OmnipathR] Loaded 75957 interactions from cache.
[2021-10-14 19:09:41] [INFO]    [wppi] Finished collecting database knowledge.
[2021-10-14 19:09:41] [INFO]    [wppi] Using all HPO annotations available.
[2021-10-14 19:09:41] [INFO]    [wppi] Calculating weighted adjacency matrix.
[2021-10-14 19:09:41] [INFO]    [wppi] Preprocessing annotations (Gene Ontology).
[2021-10-14 19:09:41] [INFO]    [wppi] Preprocessing annotations (Human Phenotype Ontology).
[2021-10-14 19:09:41] [INFO]    [wppi] Graph size: 300 nodes and 3526 edges; GO: 4024 terms, 298 genes, 13044 annotations; HPO: 2770 terms, 139 genes, 8883 annotations.
[2021-10-14 19:09:54] [INFO]    [wppi] Finished calculating weighted adjacency matrix.
[2021-10-14 19:09:54] [INFO]    [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 300).
[2021-10-14 19:10:00] [INFO]    [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 300).
[2021-10-14 19:10:00] [SUCCESS] [wppi] WPPI workflow completed.
[2021-10-14 19:10:01] [SUCCESS] [OmnipathR] Loaded 42541 interactions from cache.
Quitting from lines 124-132 (wppi_workflow.Rmd) 
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
attempt to use zero-length variable name
--- failed re-building 'wppi_workflow.Rmd'

SUMMARY: processing the following file failed:
  'wppi_workflow.Rmd'

Error: Vignette re-building failed.
Execution halted