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URL:  https://git.bioconductor.org/packages/OHCA
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nebbiolo1 Summary

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Package: OHCA
Version: 0.99.7
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OHCA
BuildTime: 21 minutes 30.73 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: OHCA_20240122124506
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: OHCA. Starting Build package.
PostProcessing: Finished Git clone. Package type: Book. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘OHCA/DESCRIPTION’ ... OK
* preparing ‘OHCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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'
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/14] index.qmd


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output file: index.knit.md

WARNING: Warning: diff of engine output timed out. No source lines will be available.

[ 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 message:
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/
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

[ 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/

[ 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

[ 7/14] pages/matrix-centric.qmd


processing file: 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

[ 8/14] pages/interactions-centric.qmd


processing file: 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

[ 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

[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/

[11/14] pages/interoperability.qmd


processing file: 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/
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

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


processing file: 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/
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

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


processing file: 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/
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

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


processing file: workflow-centros.qmd
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Quitting from lines 40-51 [unnamed-chunk-2] (workflow-centros.qmd)
Error in `h()`:
! error in evaluating the argument 'con' in selecting a method for function 'import': Unknown combination of `sample` and `format`.
  Please check which files are available from the data frame printed above.
Backtrace:
 1. BiocIO::import(...)
 4. base::.handleSimpleError(...)
 5. base (local) h(simpleError(msg, call))
Execution halted
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted

nebbiolo1 CHECK output

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