[Bioc-devel] PPA with built bioconductor packages (for continuous integration)

Martin Morgan mtmorgan at fredhutch.org
Sun Nov 9 17:26:48 CET 2014

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.


> Best,
> Laurent
> 	[[alternative HTML version deleted]]
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