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