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

Quitting from Extending_MetMashR.Rmd:534-553 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
---
Backtrace:
    ▆
 1. └─MetMashR::openbabel_structure(...)
 2.   └─struct::new_struct(...)
 3.     ├─BiocGenerics::do.call(new, L)
 4.     ├─base::do.call(new, L)
 5.     └─methods (local) `<fn>`(...)
 6.       ├─methods::initialize(value, ...)
 7.       └─methods::initialize(value, ...)
 8.         └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Extending_MetMashR.Rmd' failed with diagnostics:
invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
--- failed re-building ‘Extending_MetMashR.Rmd’

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

Quitting from annotate_mixtures.Rmd:836-869 [unnamed-chunk-27]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─struct::model_apply(SM, R)
  2. └─MetMashR::model_apply(SM, R)
  3.   └─MetMashR (local) .local(M, D, ...)
  4.     ├─struct::model_apply(M[i], D)
  5.     └─MetMashR::model_apply(M[i], D)
  6.       └─MetMashR (local) .local(M, D, ...)
  7.         ├─MetMashR::read_database(M$database)
  8.         └─MetMashR::read_database(M$database)
  9.           └─MetMashR (local) .local(obj, ...)
 10.             ├─methods::callNextMethod(obj)
 11.             │ └─base::eval(call, callEnv)
 12.             │   └─base::eval(call, callEnv)
 13.             └─MetMashR (local) .nextMethod(obj)
 14.               └─MetMashR (local) .local(obj, ...)
 15.                 └─MetMashR:::.get_cached_path(obj)
 16.                   ├─BiocFileCache::bfcdownload(...)
 17.                   └─BiocFileCache::bfcdownload(...)
 18.                     └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotate_mixtures.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘annotate_mixtures.Rmd’

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

Quitting from exploring_mtox.Rmd:107-119 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─MetMashR::read_database(MT)
  2. └─MetMashR::read_database(MT)
  3.   └─MetMashR (local) .local(obj, ...)
  4.     ├─methods::callNextMethod(obj)
  5.     │ └─base::eval(call, callEnv)
  6.     │   └─base::eval(call, callEnv)
  7.     └─MetMashR (local) .nextMethod(obj)
  8.       └─MetMashR (local) .local(obj, ...)
  9.         └─MetMashR:::.get_cached_path(obj)
 10.           ├─BiocFileCache::bfcdownload(...)
 11.           └─BiocFileCache::bfcdownload(...)
 12.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'exploring_mtox.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘exploring_mtox.Rmd’

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

Quitting from using_MetMashR.Rmd:201-210 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─MetMashR::read_source(MT)
  2. └─MetMashR::read_source(MT)
  3.   └─MetMashR (local) .local(obj, ...)
  4.     ├─MetMashR::read_database(obj)
  5.     └─MetMashR::read_database(obj)
  6.       └─MetMashR (local) .local(obj, ...)
  7.         ├─methods::callNextMethod(obj)
  8.         │ └─base::eval(call, callEnv)
  9.         │   └─base::eval(call, callEnv)
 10.         └─MetMashR (local) .nextMethod(obj)
 11.           └─MetMashR (local) .local(obj, ...)
 12.             └─MetMashR:::.get_cached_path(obj)
 13.               ├─BiocFileCache::bfcdownload(...)
 14.               └─BiocFileCache::bfcdownload(...)
 15.                 └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using_MetMashR.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘using_MetMashR.Rmd’

SUMMARY: processing the following files failed:
  ‘Extending_MetMashR.Rmd’ ‘annotate_mixtures.Rmd’ ‘exploring_mtox.Rmd’
  ‘using_MetMashR.Rmd’

Error: Vignette re-building failed.
Execution halted