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

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Tue Nov 6 16:54:13 CET 2018

In my experience, if I aggressively update my development installation of
Bioconductor (including occasional updates of R-devel when appropriate) I
can usually replicate most-all failures on the build server which has the
same OS as my local machine.  It does require aggressive updating though.

On Tue, Nov 6, 2018 at 9:17 AM Martin Morgan <mtmorgan.bioc using gmail.com>

> Thanks for the comments.
> A docker image doesn't help with differences between operating systems.
> A docker image wouldn't be practical for the build system, where there are
> 1000's of packages installed.
> A docker image would need to be updated daily, since that is what the
> build system does; you would need to pull the docker image.
> A docker image with appropriate R and base packages is available; see
> https://bioconductor.org/help/docker/ but note that these require that
> your own dependencies be installed and kept current.
> Windows builds and tests on 32 and 64 bit platforms, so can take a lot
> more time; it is difficult to differentiate between this sort of problem
> and timeouts caused by OS-specific or package issues.
> Usually avoidable problems come about because the wrong version of
> Bioconductor is in use, or because packages are not current. These can be
> checked with
>   BiocManager::version() == "3.9" # alternate: BiocManager:::isDevel()
>   BiocManager::valid()
> In the big picture I hope that we can arrive at a more continuous version
> of the builders, but that will not happen soon.
> Martin
> On 11/6/18, 8:37 AM, "Bioc-devel on behalf of 露崎 弘毅" <
> bioc-devel-bounces using r-project.org on behalf of k.t.the-answer using hotmail.co.jp>
> wrote:
>     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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