Question

Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12)

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Roger • 0

@roger-12673

Last seen 3.2 years ago

Netherlands

Hi,

After updating R to version 3.4 and Bioconductor to 3.5, ChIPQC stops working at the "Computing metrics" step. The error messages make me suspect it might be related to changes in the 'BiocParallel' package affecting the bplapply function, but that's just a guess -- what I know for sure is that it was working prior to the update. Without further ado, I leave here the message I get:

chip.samples = ChIPQC(experiment = "../DBsheet_EMCsamples.csv", annotation="hg19", bCount = TRUE)
# I have omitted the messages before the error
Computing metrics for 43 samples...
'BiocParallel' did not register default BiocParallelParams:
  comparison of these types is not implemented
Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) ==  :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In BioC 3.5, the 'force' argument was replaced by the more flexible
  'pruning.mode' argument, and is deprecated. See ?seqinfo for the
  supported pruning modes. Note that 'force=TRUE' is equivalent to
  'pruning.mode="coarse"'.

I have run the same command on another machine with a different version of R/Bioconductor and I did not encounter any issues, which supports the idea that the error can be attributed to the new version. Interestingly, however, DiffBind works just fine.

Thanks for your time.

Roger

chipqc chipqcreport • 2.4k views

ADD COMMENT • link updated 7.4 years ago by Thomas Carroll ▴ 420 • written 7.4 years ago by Roger • 0

score 0 · Answer 1 · 2017-06-15

hi Roger, Could you provide the version of BiocParallel you are using? This problem looks a little similar to this post BiocParallel/scater warning after move to R 3.4.0 . If you try and run in serial does the problem go away? register(SerialParam()) chip.samples = ChIPQC(experiment = "../DBsheet_EMCsamples.csv", annotation="hg19", bCount = TRUE) I have just updated ChIPQC (version 1.12.2) to remove the pruning.mode warning too. best, tom On Thu, Jun 15, 2017 at 2:26 PM, Roger [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Roger <https: support.bioconductor.org="" u="" 12673=""/> wrote Question: > Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12) > <https: support.bioconductor.org="" p="" 97090=""/>: > > Hi, > > After updating R to version 3.4 and Bioconductor to 3.5, ChIPQC stops > working at the "Computing metrics" step. The error messages make me suspect > it might be related to changes in the 'BiocParallel' package affecting the > bplapply function, but that's just a guess -- what I know for sure is > that it was working prior to the update. Without further ado, I leave here > the message I get: > > chip.samples = ChIPQC(experiment = "../DBsheet_EMCsamples.csv", annotation="hg19", bCount = TRUE) > # I have omitted the messages before the error > Computing metrics for 43 samples... > 'BiocParallel' did not register default BiocParallelParams: > comparison of these types is not implemented > Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) == : > missing value where TRUE/FALSE needed > In addition: Warning messages: > 1: In BioC 3.5, the 'force' argument was replaced by the more flexible > 'pruning.mode' argument, and is deprecated. See ?seqinfo for the > supported pruning modes. Note that 'force=TRUE' is equivalent to > 'pruning.mode="coarse"'. > > I have run the same command on another machine with a different version of > R/Bioconductor and I did not encounter any issues, which supports the idea > that the error can be attributed to the new version. Interestingly, > however, DiffBind works just fine, but it could > > Thanks for your time. > > Roger > > ------------------------------ > > Post tags: chipqc, chipqcreport > > You may reply via email or visit Error computing metrics with ChIPQC (Bioconductor v3.5, ChIPQC v2.1.12) >