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

Laurent Gautier lgautier at gmail.com
Sun Nov 9 16:23:59 CET 2014


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 ?



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