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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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[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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[39m[31mRegistered S3 method overwritten by 'GGally':
method from
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[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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[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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[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':
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[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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[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
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[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':
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[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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[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':
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[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
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[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
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[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':
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as.data.frame.spec_tbl_df vroom
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to: latex
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standalone: true
toc: true
number-sections: true
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graphics: true
tables: true
default-image-extension: pdf
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crossref:
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documentclass: scrreprt
papersize: letter
classoption:
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header-includes:
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block-headings: true
csl: assets/apa.csl
knitr:
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dplyr.print_max: 6
pillar.max_footer_lines: 2
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stringr.view_n: 6
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width: 77
title: Orchestrating Hi-C analysis with Bioconductor
[1mrunning xelatex - 1[22m
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[91mERROR: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/pkgbuild/texmf
tlmgr: user mode not initialized, please read the documentation!
Error: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/pkgbuild/texmf
tlmgr: user mode not initialized, please read the documentation!
at Object.onComplete (file:///opt/quarto/bin/quarto.js:98918:66)
at async renderFiles (file:///opt/quarto/bin/quarto.js:86654:16)
at async renderProject (file:///opt/quarto/bin/quarto.js:86800:25)
at async Command.fn (file:///opt/quarto/bin/quarto.js:90856:32)
at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13)
at async quarto (file:///opt/quarto/bin/quarto.js:127545:5)
at async file:///opt/quarto/bin/quarto.js:127563:9[39m
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
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