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Update DMRScan_vignette.Rmd YAML to not use leading spaces #15

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merged 1 commit into from Jan 19, 2024

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martin-g
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@martin-g martin-g commented Aug 3, 2023

YAML is space sensitive and this was leading to the following error:

* creating vignettes ... ERROR
--- re-building ‘DMRScan_vignette.Rmd’ using rmarkdown
YAML parse exception at line 10, column 0:
did not find expected <document start>
Error: processing vignette 'DMRScan_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 64
--- failed re-building ‘DMRScan_vignette.Rmd’

I am not sure why the error happens only on the Linux aarch64 builder.

YAML is space sensitive and this was leading to the following error:

```
* creating vignettes ... ERROR
--- re-building ‘DMRScan_vignette.Rmd’ using rmarkdown
YAML parse exception at line 10, column 0:
did not find expected <document start>
Error: processing vignette 'DMRScan_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 64
--- failed re-building ‘DMRScan_vignette.Rmd’
```
@martin-g
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Friendly ping!

@hpages
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hpages commented Sep 27, 2023

I am not sure why the error happens only on the Linux aarch64 builder.

Pandoc seems to be involved. Could this be because the various Bioconductor build machines use different versions of Pandoc?

@christpa It would be greatly appreciated if you could take a look at this PR. Please be aware that Bioconductor will deprecate unmaintained packages. Don't hesitate to let me know or ask on the bioc-devel mailling list if you have any questions or concerns about this. Thanks!

@martin-g
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Pandoc seems to be involved. Could this be because the various Bioconductor build machines use different versions of Pandoc?

Yes! This might be the reason!
All build nodes but kunpeng2 use Pandoc 2.7.3, while kunpeng2 uses Pandoc 3.1.2!

@martin-g
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martin-g commented Oct 5, 2023

https://bioconductor.org/checkResults/3.18/bioc-LATEST/DMRScan/ is green on Linux ARM64 too!
The builder now uses Pandoc 2.12 (the earliest version with support for Linux ARM64).

I'll leave this PR open. Hopefully it will be merged and Pandoc 3.x will be supported too!

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hpages commented Oct 5, 2023

Thanks @martin-g

@christpa Any chance you can merge this? Thanks

@christpa christpa merged commit 4e2de19 into christpa:master Jan 19, 2024
@martin-g martin-g deleted the master-1 branch January 19, 2024 07:19
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hpages commented Jan 22, 2024

Thanks @christpa. Please don't forget to push the changes to git.bioconductor.org. Thanks again!

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3 participants