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List: bioc-devel
Subject: Re: [Bioc-devel] EXTERNAL: "invalid connection" when building vignette - Windows only
From: "Ramos Perez, Marcel via Bioc-devel" <bioc-devel () r-project ! org>
Date: 2024-03-18 15:28:02
Message-ID: 4ed9fb0c-3457-4bcc-bb4b-1e233ca3066c () roswellpark ! org
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Hi Matteo,
You can get the traceback by running
rmarkdown::render("vignettes/Moonlight2R.Rmd")
Best regards,
Marcel
On 3/18/24 4:54 AM, Matteo Tiberti wrote:
> Hi Ramos,
>
> Thank you very much – this is really informative. Can I ask you how you
> got the tracback? I’m not really used at debugging this sort of issues.
>
> I can see that the EpiMix::EpiMix function we use does use foreach
> (foreach::makeCluster and %dopar%). I have no experience with foreach,
> but I had a dig, and I can see that this function cleans up the parallel
> environment with stopCluster only before just one of the several returns
> it has. So it is possible that the environment isn’t cleaned up between
> consequent function calls. We will investigate.
>
> Of course if anyone with more foreach experience wants to pinch in, they
> are very welcome
>
> Thank you again
>
>
> Matteo Tiberti
>
> *Danish Cancer Institute*
> Strandboulevarden 49
> DK-2100 Copenhagen
> *Telephone*: +45 35 25 73 07
> /– a part of the Danish Cancer Society/
>
> An image showing the Danish Cancer Society's name and logo called the
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>
> *From: *Ramos Perez, Marcel <Marcel.RamosPerez@RoswellPark.org>
> *Date: *Friday, 15 March 2024 at 22.44
> *To: *bioc-devel@r-project.org <bioc-devel@r-project.org>
> *Cc: *Matteo Tiberti <tiberti@cancer.dk>
> *Subject: *Re: EXTERNAL: [Bioc-devel] "invalid connection" when building
> vignette - Windows only
>
> 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
> <https://secure-web.cisco.com/1YD8SZqXAX191pf8cgoBfpAmG1_h-Hr7uAOYm9GgC6_JozBpssa_-Q \
> rhbhIRLxi2NhF5HBbCJbg4ySbVEqr8NUsdQ9psLWqnIJY0Fdux6_jooJSOSDFG2BlOoovrtKD8g6ep2RQUlW \
> TETFAaZjH1usKFjEmxGDLJ6M87WHofw9OsELBCRJNPfg1Jt2B8S2K6uBgkbsutqEfffAA19EaJn2MruFxo8r \
> CnddjHiyJuF73_nKKEIxPdTqffRtjYIfr2SJ-FtT_C_mvPVdOTnggJbZGhvPjau9r8RIYBja69qiiBoXBK1AyC_i40zCDVUfqqW/https%3A%2F%2Fstackoverflow.com%2Fa%2F67497500>
>
> 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 \
> <https://secure-web.cisco.com/1By4iDLoonNq9oCuWZXPosebkSm_dNmB68WHlRYlsuY0mLDWGPavDC \
> ZHWMJvKAbZM1cUy7qzqWl81dRjtWNgIW6xGgBozsyO_0Zg2WfSH1JLZHfgm870r7PHbNG8qdpj0FH23FskTE \
> ZgBycY8KTUcSW0UWZmBSoP1eeDox_wBKsvlsUk_XhhBOu76pmj26qrc6WokVrZnHWSQ9rQX6aGhI2ubdN5gZ \
> OHE_iL3JU0cnM_0i3SK4SWrkiIsVBCghdawutrILEEHaZRLsyLaaVIgJNMb1xLd2NUrl006Q4Yn-2Mlu0HPh \
> jLiUqayMhx7s9MQ/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.18%2Fdata%2Fexperiment%2Fsrc%2Fcontrib%2FsesameData_1.20.0.tar.gz>'
>
>
>
> trying URL
> 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz \
> <https://secure-web.cisco.com/1By4iDLoonNq9oCuWZXPosebkSm_dNmB68WHlRYlsuY0mLDWGPavDC \
> ZHWMJvKAbZM1cUy7qzqWl81dRjtWNgIW6xGgBozsyO_0Zg2WfSH1JLZHfgm870r7PHbNG8qdpj0FH23FskTE \
> ZgBycY8KTUcSW0UWZmBSoP1eeDox_wBKsvlsUk_XhhBOu76pmj26qrc6WokVrZnHWSQ9rQX6aGhI2ubdN5gZ \
> OHE_iL3JU0cnM_0i3SK4SWrkiIsVBCghdawutrILEEHaZRLsyLaaVIgJNMb1xLd2NUrl006Q4Yn-2Mlu0HPh \
> jLiUqayMhx7s9MQ/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.18%2Fdata%2Fexperiment%2Fsrc%2Fcontrib%2FsesameData_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
>
> [An image showing the Danish Cancer Society's name and logo called
> the bow in red font. Displayed in
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> _______________________________________________
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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
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee
> or agent responsible for the delivery of this message to the intended
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> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
--
Marcel Ramos Pérez
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263
This email message may contain legally privileged and/or confidential information. \
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