----- Original Message ----- > From: "Martin Morgan" <mtmor...@fredhutch.org> > To: "Laurent Gautier" <lgaut...@gmail.com>, bioc-devel@r-project.org > Sent: Sunday, November 9, 2014 8:26:48 AM > Subject: Re: [Bioc-devel] PPA with built bioconductor packages (for > continuous integration) > > 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, ...);
Just to add to the mix of options, it's possible to run R CMD INSTALL --build on a source tarball on Linux and it will create a 'binary' version that is already compiled. The problem with this is (AFAIK) there is no corresponding package type that can be used with install.packages(); otherwise the simplest solution would be to add a CRAN-style repos containing these "binaries". Maybe R could be patched to allow this? But it's possible that the requirements for Linux "binaries" could vary depending on many things: cpu type (intel or solaris, or...), architecture (i386, x64), presence/absence of BLAS/LAPACK, etc etc etc. This suggests that a vm or container-based approach might be better. Dan > 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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
