[Bioc-devel] rfaRm package

Jennifer Wokaty Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu
Mon Jun 26 22:26:43 CEST 2023

Hi Lara,

Today, I tried R CMD build​ on your package on our Linux release builder and got the following:

~/bbs-3.17-bioc/R/bin/R CMD build rfaRm
* checking for file ‘rfaRm/DESCRIPTION’ ... OK
* preparing ‘rfaRm’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rfaRm.Rmd’ using rmarkdown

Quitting from lines 74-83 [unnamed-chunk-3] (rfaRm.Rmd)
Error: processing vignette 'rfaRm.Rmd' failed with diagnostics:
Timeout was reached: [rfam.org] SSL connection timeout
--- failed re-building ‘rfaRm.Rmd’

SUMMARY: processing the following file failed:

Error: Vignette re-building failed.
Execution halted

However, I see that it actually passed the build today on that same machine but failed on R CMD check, so it's possible that that the problem is intermittent due to connection issues.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Selles Vidal, Lara <lara.selles12 using imperial.ac.uk>
Sent: Monday, June 19, 2023 9:37 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] rfaRm package

* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *

Dear all,

My rfaRm package has been giving TIMEOUT in the build results on all plaforms recently. I have been tried to debug the issue, but I am unable to reproduce the problem locally. The build report only seems to indicate that it times out while building vignettes (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_rfaRm_merida1-2Dbuildsrc.html&d=DwIFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=qTwdJxyJM_TNb3T9s_tfKmSX0e7aNvkVIBXATnsYJRaFl9_9IE9R7tqCSRJcDRJH&s=VhKun5uNWjqnt5WsUNKIC1Z6vYVC3LnChzZWpGFvQfg&e= ). Would there be any way to specifically find out at which point of building the vignette the timing out is taking place?

Thanks a lot in advance!

Best wishes,
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