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

Tim Triche, Jr. tim.triche at gmail.com
Sun Nov 9 17:14:50 CET 2014

Yes.  The same sort of thing happens when I send code to others. The library dependencies often take longer to install than the code takes to run, and these are not trivial analyses (thousands of cases across dozens of studies with millions to billions of data points).  The idea of a PPA in a VM (or perhaps even better, something like a Kubernetes pod) is very attractive. 


> On Nov 9, 2014, at 7:23 AM, Laurent Gautier <lgautier at gmail.com> 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 ?
> Best,
> Laurent
>    [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list