[Bioc-devel] Time out in R CMD check

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Wed May 30 14:05:20 CEST 2018

We encourage the communication on an issue and the assigned review to occur on the issue tracker.  Your reviewer could also provide some suggestions.

If possibly ideally the solution would be to provide a smaller example set so that all the functions could be performed within the time constraint.  A small toy example set often shows functionality well enough than a full set.

Please ask further questions in your issue thread.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Xu Ren <xuren2120 using gmail.com>
Sent: Sunday, May 27, 2018 3:34:03 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Time out in R CMD check

Hi all,

I submitted a package call methylGO which is used to perform gene set
testing with length bias adjustment for DNA methylation data. One important
step is to get gene symbol and their corresponding CpG IDs on Illumina 450K
array. I get the CpG IDs from IlluminaHumanMethylation450kanno.ilmn12.hg19
package using *getAnnotation *function in minfi package. But this process
takes some time, which makes R CMD check exceed 5 min time limit. However,
getting the annotation is an essential step and it cannot be avoided. Is
this possible for the time limit to be extended?

Xu Ren

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