[Bioc-devel] EXTERNAL: "invalid connection" when building vignette - Windows only

[Ramos Perez, Marcel]

Hi Matteo,

I was also able to reproduce on Bioc 3.18 on Windows with a traceback (see below).

It may be that there are symbol clashes between parallel runs in the
`foreach:::.foreachGlobals` environment as described in
https://stackoverflow.com/a/67497500

Clearing the symbols in that environment alleviates the problem temporarily
until running the chunk in line 1124 where the same error occurs.

Someone with more experience using `foreach` and socket clusters may be able to help.

Note that the code should be running on either one or two cores by default.

Best regards,

Marcel

```

processing file: Moonlight2R.Rmd
  |.......................                            |  45% [unnamed-chunk-20]
Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)

Error in `summary.connection()`:
! invalid connection
Backtrace:
  1. Moonlight2R::GMA(...)
  2. EpiMix::EpiMix(...)
       at Moonlight2R/R/GMA.R:117:3
  3. EpiMix:::MethylMix_MixtureModel(...)
  4. ... %dopar% ...
     ...
  7. parallel:::sendCall(cl[[i]], fun, list(...))
  8. parallel:::postNode(...)
 10. parallel:::sendData.SOCKnode(...)
 11. base::serialize(data, node$con)
 13. base::summary.connection(connection)
Execution halted

```

On 3/15/24 6:05 AM, Matteo Tiberti via Bioc-devel wrote:
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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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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