ChIPseeker failing on r-devel on CRAN checks
0
0
Entering edit mode
@eonurk
Last seen 3.6 years 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 • 1.2k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 751 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6