[Bioc-devel] PPA with built bioconductor packages (for continuous integration)
mtmorgan at fredhutch.org
Sun Nov 9 17:26:48 CET 2014
On 11/09/2014 07:23 AM, Laurent Gautier wrote:
> Continuous integration is a convenient way to automate some of the steps
> necessary to ensure quality software.
> Popular ways to do it create a vanilla virtual machine 9VM) with a Linux
> distribution, and scripts prepares the VM with 3rd-party dependencies
> required by the software. For example, the popular CI system Travis for
> github creates by default a VM running ubuntu, and dependencies can be
> installed with `apt-get install`.
> When developing software that requires CRAN/bioconductor, the latest R is
> available precompiled but the R packages must be downloaded installed from
> This can take a relatively long time. On a recent project over 80% of the
> time is spent downloading/installing the R/BioC packages. The remaining is
> building the code and running the unit tests.
> Having a Personal Package Archive (PPA) with bioconductor packages already
> compiled would both speed up the process and make the use of continuous
> integration by projects relying on bioconductor packages easier.
> Is this something others would like to have, and is this something that
> bioconductor would see to its mission to provide / help provide quality
> software and be able to host ?
It would be interesting to catalogue objectives (e.g., development vs.
reproducibility) and available alternatives (e.g., PPA, docker / Rocker, AMI,
existing or possible cloud services [such as the Bioc 'single package builder'
used to build and check new package submissions, or travis itself], the Becker
repository management scheme Michael and Gabe mention, ...); if there is a clear
path forward satisfying some plurality of users without too many technical
obstacles then it might fall within the Bioc purview; my initial sense is that
there is not a consensus on use cases or viable implementations, but I can be
In terms of Tim's post, getting your colleague to use a PPA / existing
alternative (e.g., the Bioc AMI,
http://bioconductor.org/help/bioconductor-cloud-ami/ which comes with Rstudio
server installed...) is not likely to be easier / faster than getting them to
download / install relevant R / Bioc packages. One interesting possibility is a
'hosted' bioconductor with sufficient computational resources on the back-end
and Rstudio server on the front end; this is not impossible to imaging seeking
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