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This page was generated on 2026-02-24 11:58 -0500 (Tue, 24 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4891
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2190/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.38.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2026-02-23 13:45 -0500 (Mon, 23 Feb 2026)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: RELEASE_3_22
git_last_commit: 29c7106
git_last_commit_date: 2025-10-29 10:27:16 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for TCGAbiolinks in R Universe.

BUILD results for TCGAbiolinks on nebbiolo2

To the developers/maintainers of the TCGAbiolinks package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAbiolinks.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TCGAbiolinks
Version: 2.38.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 TCGAbiolinks
StartedAt: 2026-02-23 20:27:40 -0500 (Mon, 23 Feb 2026)
EndedAt: 2026-02-23 20:32:30 -0500 (Mon, 23 Feb 2026)
EllapsedTime: 289.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 TCGAbiolinks
###
##############################################################################
##############################################################################


* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* preparing ‘TCGAbiolinks’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysis.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Connection refused),Network.Socket.connect: <socket: 18>: does not exist (Connection refused)]))
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘analysis.Rmd’

--- re-building ‘casestudy.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Connection refused),Network.Socket.connect: <socket: 18>: does not exist (Connection refused)]))
Error: processing vignette 'casestudy.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘casestudy.Rmd’

--- re-building ‘classifiers.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Network unreachable),Network.Socket.connect: <socket: 18>: does not exist (Connection refused),Network.Socket.connect: <socket: 18>: does not exist (Connection refused)]))
Error: processing vignette 'classifiers.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘classifiers.Rmd’

--- re-building ‘clinical.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'clinical.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘clinical.Rmd’

--- re-building ‘download_prepare.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'download_prepare.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘download_prepare.Rmd’

--- re-building ‘extension.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'extension.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘extension.Rmd’

--- re-building ‘index.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'index.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘index.Rmd’

--- re-building ‘mutation.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'mutation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘mutation.Rmd’

--- re-building ‘query.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'query.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘query.Rmd’

--- re-building ‘stemness_score.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'stemness_score.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘stemness_score.Rmd’

--- re-building ‘subtypes.Rmd’ using rmarkdown
Could not fetch https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css
HttpExceptionRequest Request {
  host                 = "maxcdn.bootstrapcdn.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/font-awesome/4.4.0/css/font-awesome.min.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "maxcdn.bootstrapcdn.com" [Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Network unreachable),Network.Socket.connect: <socket: 19>: does not exist (Connection refused),Network.Socket.connect: <socket: 19>: does not exist (Connection refused)]))
Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘subtypes.Rmd’

SUMMARY: processing the following files failed:
  ‘analysis.Rmd’ ‘casestudy.Rmd’ ‘classifiers.Rmd’ ‘clinical.Rmd’
  ‘download_prepare.Rmd’ ‘extension.Rmd’ ‘index.Rmd’ ‘mutation.Rmd’
  ‘query.Rmd’ ‘stemness_score.Rmd’ ‘subtypes.Rmd’

Error: Vignette re-building failed.
Execution halted