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List:       bioc-devel
Subject:    [Bioc-devel] "invalid connection" when building vignette - Windows only
From:       Matteo Tiberti via Bioc-devel <bioc-devel () r-project ! org>
Date:       2024-03-15 10:05:21
Message-ID: 638460939730394388.58600d898db34ca0bc6294ad05e07713#DPG#Sh2bfCsxFxL0q51ljpNBAAAnG2hWG6TXHKe56Q5rmriTI8W6wcs9hvY85eGQVVcE () cancer ! dk
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Dear developers,

we've been getting a build fail for our Moonlight2R package on Windows only, during \
vignette build in CHECK, which just prints out an "invalid connection" error:

Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)
Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'Moonlight2R.Rmd'

The following snippet is the code chunk that causes the fail:

data("dataMethyl")
data("dataFilt")
data("dataPRA")
data("DEGsmatrix")
data("LUAD_sample_anno")
data("NCG")
data("EncodePromoters")
data("MetEvidenceDriver")

# Subset column names (sample names) in expression data to patient level
pattern <- "^(.{4}-.{2}-.{4}-.{2}).*"
colnames(dataFilt) <- sub(pattern, "\\1", colnames(dataFilt))

dataGMA <- GMA(dataMET = dataMethyl, dataEXP = dataFilt,
               dataPRA = dataPRA, dataDEGs = DEGsmatrix,
               sample_info = LUAD_sample_anno, met_platform = "HM450",
               prevalence_filter = NULL,
               output_dir = "./GMAresults", cores = 1, roadmap.epigenome.ids = \
"E096",  roadmap.epigenome.groups = NULL)

I could reproduce this fail on my local Windows machine (on release rather than devel \
at the moment), so it's probably not an issue with the builders. It builds and runs \
successfully on Linux, both on devel and release. I have also tried running the same \
code by hand on the R prompt, and that completes successfully.

The error I get when trying to build the vignette manually is possibly more \
informative:


> devtools::build_vignettes('../Downloads/Moonlight2R-devel/Moonlight2R-devel/')

ℹ Installing Moonlight2R in temporary library
ℹ Building vignettes for Moonlight2R
--- re-building 'Moonlight2R.Rmd' using rmarkdown

processing file: Moonlight2R.Rmd
  |.......................                            |  45% [unnamed-chunk-20]trying \
URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz'




trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz'
 Content type 'application/x-gzip' length 1975798 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

* installing *source* package 'sesameData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location


** testing if installed package can be loaded from final location



** testing if installed package keeps a record of temporary installation path
* DONE (sesameData)

The downloaded source packages are in
        'C:\Users\Work\AppData\Local\Temp\RtmpmsVLSL\downloaded_packages'

Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)

Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'Moonlight2R.Rmd'

SUMMARY: processing the following file failed:
  'Moonlight2R.Rmd'


so it installs the sesameData package (because of \
ExperimentHub::ExperimentHub()[['EH3675']]) , and then fails like that.

We have very little experience in development under Windows and are a bit stumped on \
what might be the problem; do you know whether this error message comes from anything \
in particular or do you have any further idea on how to troubleshoot this?

I assume the error message does not refer to connecting to some server on the \
internet, since all works fine on Linux and I can reproduce the problem from \
different machines/connections. But happy to hear your thoughts

Thank you and kind regards,

Matteo Tiberti

Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society

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