The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: Build error: could not find function "bplapply"
0
gravatar for Charles Plessy
13 months ago by
Japan
Charles Plessy90 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 • 268 views
ADD COMMENTlink modified 13 months ago by Martin Morgan ♦♦ 22k • written 13 months ago by Charles Plessy90
Answer: Build error: could not find function "bplapply"
2
gravatar for Martin Morgan
13 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k 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 13 months ago • written 13 months ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 201 users visited in the last hour