[Bioc-devel] Error in methylclockData package

Wed Jun 12 15:35:19 CEST 2024

I can't reproduce either of these and when I check the resources on the builders they load successfully so doesn't appear to be a caching issue.  I would expect them to clear up on the next run of the builders.   Let's see what happens on the next run and if they continue to error I can look further into it.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Morgan, Michael via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, June 12, 2024 4:02 AM
To: Dolors Pelegrí <dolors.pelegri using isglobal.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Error in methylclockData package

Dear BioC Team,
I am receiving a similar error from the MouseThymusAgeing package:
> smart.data <- MouseSMARTseqData(samples = "day1")
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for documentation
loading from cache
field not found in version - adding
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for documentation
loading from cache
Error: failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format
Execution halted

Which is subsequently propagating through to errors in miloR on nebbiolo1 only (Windows and Mac build servers are unaffected).

Quitting from lines 47-50 [unnamed-chunk-2] (milo_contrasts.Rmd)
Error: processing vignette 'milo_contrasts.Rmd' failed with diagnostics:
failed to load resource
  name: EH4592
  title: SMARTseq processed counts (day 1)
  reason: unknown input format

Is this an issue with caching files?

Regards
Mike Morgan

Pronouns: He/Him
Lecturer
6.17, Institute of Medical Sciences
School of Medicine, Medical Sciences & Nutrition
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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Dolors Pelegr�dolors.pelegri using isglobal.org>
Date: Wednesday, 12 June 2024 at 08:38
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Error in methylclockData package
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Dear Bioconductor team,

I have seen that the methylclockData package gives an error when loading
the EH6082 resource, the error is:

get_TestDataset()
see ?methylclockData and browseVignettes('methylclockData') for
documentation
loading from cache
Warning in grepl("RD[ABX][2-9]\n", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\n", magic) : input string 1 is invalid
Warning in grepl("RD[ABX][2-9]\r", magic) :
 unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\r", magic) : input string 1 is invalid
Warning in gsub("[\n\r]*", "", magic) :
 unable to translate '<89>HDF
' to a wide string
Error: failed to load resource
 name: EH6082
 title: Test Dataset
 reason: error in evaluating the argument 'x' in selecting a method for
function 'get': input string 1 is invalid
Execution halted

Full Bioconductor Checks:
https://bioconductor.org/checkResults/3.19/data-experiment-LATEST/methylclockData/nebbiolo1-checksrc.html<https://secure-web.cisco.com/1jf9ytfpmFmocyAfOpBw_grzcU1oGr3iMOG6l_DdAq3dFaXdA3mxJtS3itQFxhW5HqVb5DBmknP6RrWxXs_am2zYwBdHCwVEP5RiqO03tGY2lfgcpsZqPcpHwyzetaTDW5KHZMdggG9y2Fwdz4j1nZfPKukOL-oZDF0Ies6Zv2wlXf3mZZd7gZet2L6OujW_bIzdrxd4Kn1OVdLk8eFpIbs8RWjuOxENmQYJ6jt9sNlLVw2Q01eY8Z0vXXEyRZqr5vfCtbhoKVhtwm6J-1iwDzTLUypFqzRm-Cy8_YiNehVHdyw6rhkcK3Tmd_R4QQf3b/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fdata-experiment-LATEST%2FmethylclockData%2Fnebbiolo1-checksrc.html>

I don't know the reason or how I could solve it, I've searched the
distribution list and I haven't found any similar error. Could you please
give me some guidance to solve the error?

Best,

--

Dolors Pelegr�is�ioinformatics

*IS**Global*

Barcelona Institute for Global Health

Barcelona Biomedical Research Park (PRBB)

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Tel. +34 93 2147351

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