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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmicsMLRepoR
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* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* preparing ‘OmicsMLRepoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Browse_cBioPortal.Rmd’ using rmarkdown

Quitting from Browse_cBioPortal.Rmd:118-130 [breast_cancer]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─cbio %>% tree_filter(cancer_type, "breast cancer")
 2. └─OmicsMLRepoR::tree_filter(., cancer_type, "breast cancer")
 3.   └─utils::read.csv(file.path(dir, fname), header = TRUE)
 4.     └─utils::read.table(...)
 5.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Browse_cBioPortal.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Browse_cBioPortal.Rmd’

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

Quitting from Quickstart.Rmd:199-205 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
     ▆
  1. ├─... %>% ...
  2. ├─curatedMetagenomicData::returnSamples(...)
  3. │ ├─curatedMetagenomicData::mergeData(...)
  4. │ └─curatedMetagenomicData::curatedMetagenomicData(...)
  5. │   ├─AnnotationHub::query(ExperimentHub(), resources)
  6. │   └─ExperimentHub::ExperimentHub()
  7. │     └─AnnotationHub::.Hub(...)
  8. │       └─base::tryCatch(...)
  9. │         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10. │           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11. │             └─value[[3L]](cond)
 12. │               └─base::stop(...)
 13. └─base::.handleSimpleError(...)
 14.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Quickstart.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘Quickstart.Rmd’

--- re-building ‘tree_filter.Rmd’ using rmarkdown
--- finished re-building ‘tree_filter.Rmd’

SUMMARY: processing the following files failed:
  ‘Browse_cBioPortal.Rmd’ ‘Quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted