Question: Build error: could not find function "bplapply"
gravatar for Charles Plessy
17 months ago by
Charles Plessy110 wrote:

The current version (1.21.4) of the CAGEr package fails to check with the following error:

* checking examples ... ERROR
Running examples in ‘CAGEr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CustomConsensusClusters
> ### Title: Expression levels of consensus cluster
> ### Aliases: CustomConsensusClusters
> ###   CustomConsensusClusters,CAGEexp,GRanges-method
> ### ** Examples
> cc <- consensusClustersGR(exampleCAGEexp)
> CustomConsensusClusters(exampleCAGEexp, cc)
Error in bplapply(seq_len(nblock), function(b) { : 
  could not find function "bplapply"
Calls: CustomConsensusClusters ... .CCtoSE -> .CCtoSE -> [ -> rowSums -> rowSums -> blockApply
Execution halted

But I do not understand why bplapply is not found since:

  • CAGEr Imports BiocParallel,
  • CAGEr importFrom(BiocParallel,bplapply), and
  • CustomConsensusClusters does not use bplapply.

What am I missing ?

biocparallel build report • 335 views
ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 23k • written 17 months ago by Charles Plessy110
Answer: Build error: could not find function "bplapply"
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Ask questions about package development on the bioc-devel mailing list, rather than on this end-user support site.

The problem is that the DelayedArray package, which was recently updated to use BiocParallel, does not import bplapply; this is a bug and will be fixed; you do not need to do anything with CAGEr. Thanks for the report; I opened an issue on the DelayedArray package repository..

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