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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmSparseNet
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* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown

Quitting from example_brca_logistic.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. └─base::library(TCGAutils)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘example_brca_logistic.Rmd’

--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown

Quitting from example_brca_protein-protein-interactions_survival.Rmd:28-53 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. └─base::library(TCGAutils)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example_brca_protein-protein-interactions_survival.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘example_brca_protein-protein-interactions_survival.Rmd’

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

Quitting from example_brca_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. └─base::library(TCGAutils)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘example_brca_survival.Rmd’

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

Quitting from example_prad_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. └─base::library(TCGAutils)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example_prad_survival.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘example_prad_survival.Rmd’

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

Quitting from example_skcm_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. └─base::library(TCGAutils)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAutils':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘example_skcm_survival.Rmd’

--- re-building ‘separate2GroupsCox.Rmd’ using rmarkdown
--- finished re-building ‘separate2GroupsCox.Rmd’

SUMMARY: processing the following files failed:
  ‘example_brca_logistic.Rmd’
  ‘example_brca_protein-protein-interactions_survival.Rmd’
  ‘example_brca_survival.Rmd’ ‘example_prad_survival.Rmd’
  ‘example_skcm_survival.Rmd’

Error: Vignette re-building failed.
Execution halted