[Bioc-devel] About the reproducibility of BioC server environment

[露崎 弘毅]

Dear Bioc Core Team

I have created many Bioconductor packages, but it is always hard to pass the R CMD CHECK/BiocCheck.

Especially, it is still difficult to construct the identical environment of single/daily package builder in the local machine.

Sometimes the error is caused by the difference of the OS (e.g. Windows ↔︎ Linux, Max), but it is very difficult to trace the reason in the local machine.

In the "daily" package builder case, the code can be tested only one time per day, and it will slow down the package development speed.

I have often experienced that the BiocCheck in tokay1 (Windows) is failed due to the CheckTime, but it is difficult to distinguish whether the error is caused by my source-code or the machine is just busy for the task of other packages.


Why don't you create the docker containers for the single/daily package builder?
https://www.bioconductor.org/help/docker/

I think that it will be very helpful for many BioC developers.

I want to use the system like below.


docker run bioconductor/single_windows
docker run bioconductor/single_linux
docker run bioconductor/single_mac
docker run bioconductor/daily_windows
docker run bioconductor/daily_linux
docker run bioconductor/daily_mac


Koki Tsuyuzaki

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