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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data dce
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* checking for file ‘dce/DESCRIPTION’ ... OK
* preparing ‘dce’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dce.Rmd’ using rmarkdown
INFO [2025-03-21 22:14:09] Processing kegg

Quitting from dce.Rmd:241-243 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dce()`:
! Not all nodes have expression vector in WT data
---
Backtrace:
    ▆
 1. ├─dce::dce(brca_pathway, t(brca_wt), t(brca_mt))
 2. └─dce::dce(brca_pathway, t(brca_wt), t(brca_mt))
 3.   ├─dce::dce(...)
 4.   └─dce::dce(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'dce.Rmd' failed with diagnostics:
Not all nodes have expression vector in WT data
--- failed re-building ‘dce.Rmd’

--- re-building ‘pathway_databases.Rmd’ using rmarkdown
INFO [2025-03-21 22:14:17] Processing pathbank
INFO [2025-03-21 22:14:46] Processing kegg

Quitting from pathway_databases.Rmd:63-80 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `buildEdgeList()`:
! attempt to set index 12/12 in SET_STRING_ELT
---
Backtrace:
     ▆
  1. ├─BiocGenerics::lapply(...)
  2. └─base::lapply(...)
  3.   └─global FUN(X[[i]], ...)
  4.     └─dce::plot_network(...)
  5.       ├─purrr::map_dfr(...)
  6.       │ └─purrr::map(.x, .f, ...)
  7.       │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  8.       │     └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
  9.       └─Rgraphviz::agopen(as(tmp, "graphNEL"), name = "foo", layoutType = "dot")
 10.         └─Rgraphviz::buildEdgeList(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pathway_databases.Rmd' failed with diagnostics:
attempt to set index 12/12 in SET_STRING_ELT
--- failed re-building ‘pathway_databases.Rmd’

SUMMARY: processing the following files failed:
  ‘dce.Rmd’ ‘pathway_databases.Rmd’

Error: Vignette re-building failed.
Execution halted