##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OHCA
###
##############################################################################
##############################################################################


* checking for file ‘OHCA/DESCRIPTION’ ... OK
* preparing ‘OHCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.knit'
Could not fetch http://bioconductor.org/books/3.23/OHCA
HttpExceptionRequest Request {
  host                 = "bioconductor.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/books/3.23/OHCA"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'stub.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/14] index.qmd


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[ 2/14] pages/preamble.qmd

[ 3/14] pages/principles.qmd


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output file: principles.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
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In readLines(input) : incomplete final line found on 'principles.qmd'

[ 4/14] pages/data-representation.qmd


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output file: data-representation.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 5/14] pages/parsing.qmd


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output file: parsing.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 6/14] pages/visualization.qmd


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output file: visualization.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 24 then 26
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[ 7/14] pages/matrix-centric.qmd


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output file: matrix-centric.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 24 then 26
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[ 8/14] pages/interactions-centric.qmd


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output file: interactions-centric.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 9/14] pages/topological-features.qmd


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output file: topological-features.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[10/14] pages/disseminating.qmd


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output file: disseminating.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[11/14] pages/interoperability.qmd


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output file: interoperability.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 10 then 12

[12/14] pages/workflow-yeast.qmd


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output file: workflow-yeast.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 10 then 12

[13/14] pages/workflow-chicken.qmd


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output file: workflow-chicken.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 10 then 12

[14/14] pages/workflow-centros.qmd


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output file: workflow-centros.knit.md

Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
Warning: stack imbalance in 'vapply', 10 then 12

Output created: docs/index.html

mkdir -p ../inst/doc && mv ../inst/docs ../inst/doc/book
SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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