[Bioc-devel] Testing the srnadiff package with R CMD check takes lots of time

[Matthias Zytnicki]

Dear everyone,


I have difficulties trying to decrease the time spent to check my package, srnadiff (for reproducibility, you can get the GitHub repo from https://github.com/mzytnicki/srnadiff, on the devel branch).


I tried to reduce the tests to 2 files (for reproducibility: test_annotation.R and test_pvalues.R).


When I use devtools::check(), the "checking tests" step takes 29 minutes.  With all the files, it takes more than one hour. Same goes with R CMD check on the built package. On the BioC check platform, it reaches the time limit.


When I use devtools::test(), the same tests takes 8 seconds.


Now, on the computer of my colleague, trying to reproduce the BioC environment variables, the whole devtools::check takes a few minutes.


I am puzzled by the discrepancy, and would like to reduce this time.

Does anyone have a suggestion about how I could proceed?


I used profvis with the command  p <- profvis::profvis({foo <- devtools::check()})

It seems that most of the time is spent on ".Call" (with no other sub-function called), and I cannot interpret this.


I thank you very much for your help.


Best regards,


Matthias.

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