ChIPseeker failing on r-devel on CRAN checks
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@eonurk
Last seen 14 months ago
Farmington

Hello everyone,

I have a package called cinaR on CRAN which depends on ChIPseeker.

Recently, I got a mail from CRAN team about building error and warnings. See here.

Therefore, I sent an update (which worked fine on my setup, with --as-cran check, and on winbuilder) but again failed with the same warning.

>> Experiment type: ATAC-Seq
>> Matrix is filtered!

Quitting from lines 53-55 (cinaR.Rmd)
Error: processing vignette 'cinaR.Rmd' failed with diagnostics:
error in evaluating the argument 'args' in selecting a method for function 'do.call': GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
--- failed re-building 'cinaR.Rmd'

and between the last print ("Matrix is filtered!") and the error, I only initialize a Granges object and required TxDb objects (lines 318-360 of cinaR.R). Next, I send these objects to annotatePeak function from ChIPseeker which normally prints several things to console, yet in my case does not. Also, when I told about this to CRAN team, they told me "...neither ChIPseeker nor your package can be installed in R-devel", which seemed to me like the core of my problem.

So, is there anything I could do about this situation?

Thank you for your replies,

Onur

ChIPseeker cinaR • 489 views
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Hi Onur,

You might get more traction by posting this to the Bioconductor developers mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel). This forum is intended more for user facing questions, and software development is addressed on that mailing list.

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Thank you very much Mike, I will try my luck there as well.

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