Question: Error: BiocParallel errors; first error: invalid 'times' value
1
gravatar for skhalid7
17 months ago by
skhalid710
skhalid710 wrote:

I'm running the package MBASED which uses various bioconductor packages. When I run MBASED on a small dataset it runs fine however when I run it on larger datasets it throws the following error:

Error: BiocParallel errors
  element index: 32, 33, 34, 35, 36, 37, ...
  first error: invalid 'times' value
In addition: Warning message:
stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit

Furthermore it sometimes also throws the error:

Error in serialize(data, node$con, xdr = FALSE) : ignoring SIGPIPE signal

I'm not sure what these errors mean and don't know how to go about debugging them. Any help on this would be appreciated.

Thank you,

Shareef

biocparallel mbased • 381 views
ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 23k • written 17 months ago by skhalid710
Answer: Error: BiocParallel errors; first error: invalid 'times' value
0
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

The MBASED code is using BiocParallel to evaluate some code chunks on additional processes. It could be that the evaluation on these code chunks is failing because of a problem with your data or the implementation in MBASED. Alternatively, it could be that the amount of data being transferred between processes is too large. In either case, you could try providing the argument BPPARAM = BiocParallel::SerialParam() to the MBASED function that you are calling. This will cause the code to run on only one processor, slowing down the calculation but allowing you to see what (under scenario 1) the problem is. If there is no problem under serial mode, then probably a fully reproducible example would be required -- your data, plus the exact code that you're running. In the latter case, it would help to make sure that you are running the current version of Bioconductor and that your packages are up to date. Use BiocInstaller::biocVersion() to see the version of Bioconductor (and compare to, e.g., http://bioconductor.org/install/) and BiocInstaller::biocValid() to make sure that your packages are current and from a single Bioconductor release.

ADD COMMENTlink written 17 months ago by Martin Morgan ♦♦ 23k
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