On Nov 9, 2014 8:06 PM, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote: > > > > ----- 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?
This would be a solution to the problem, and more general one ( a PPA would be possibly restricted to Ubuntu or Debian. For some similar situations with python packages I am using Python " wheels", which are the same as the proposed binary R packages. Laurent > 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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel