On 11/09/2014 07:23 AM, Laurent Gautier wrote:
Hi,
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
source.
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
convinced otherwise...
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
funding for.
Martin
Best,
Laurent
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