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R CMD BUILD
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* 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/
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[31moutput file: index.knit.md
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[31moutput file: principles.knit.md
[39m[31mConsider 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/
[39m[31mWarning message:
In readLines(input) : incomplete final line found on 'principles.qmd'
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[31moutput file: data-representation.knit.md
[39m[31mConsider 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/
[39m[31mRegistered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
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[31moutput file: parsing.knit.md
[39m[31mConsider 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/
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[31moutput file: visualization.knit.md
[39m[31mConsider 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/
[39m[31mRegistered 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
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[31moutput file: matrix-centric.knit.md
[39m[31mConsider 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/
[39m[31mRegistered 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
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[31moutput file: interactions-centric.knit.md
[39m[31mConsider 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/
[39m[31mRegistered 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
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[31moutput file: topological-features.knit.md
[39m[31mConsider 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/
[39m[31mRegistered 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
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[31m
Quitting from lines 90-93 [unnamed-chunk-5] (disseminating.qmd)
[39m[31mError in `.new_IRanges_from_start_width()`:
! 'start' and 'width' must be numeric vectors
Backtrace:
1. BiocIO::import(pairs_f)
2. BiocIO::import(pairs_f)
4. BiocIO::import(FileForFormat(con), ...)
6. HiCExperiment::import(con, ...)
7. HiCExperiment:::.pairs2gi(con, ...)
9. IRanges::IRanges(anchors1[[2]], width = 1)
10. IRanges:::.new_IRanges(start = start, end = end, width = width)
11. IRanges:::.new_IRanges_from_start_width(start, width)
[39m[31mExecution halted
[39mmake: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted