Hi Ross,
you are absolutely right. My download_store repository is exactly for this purpose.
https://github.com/bgruening/download_store
If you are interested we could integrate your additional magic into the notebook.
Thanks, Bjoern
Am 11.01.2015 um 01:33 schrieb Ross:
Hi, Björn, Looks pretty similar! Aren't the links your notebook generates transient? I think if you put them into a tool_dependencies.xml, they will fail permanently immediately after any of the package authors updates one of the relevant svn repositories?
AFAIK, it looks like the whole BioC/CRAN infrastructure is automated so a link that works today like http://cran.fhcrc.org/src/contrib/Rcpp_0.11.3.tar.gz will fail when Rcpp next gets updated and Rcpp_0.11.3.tar.gz is migrated to http://cran.fhcrc.org/src/contrib/00Archive/Rcpp/ with a replacement (eg) http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz appearing in the contrib directory?
That's why my more complex script downloads all the latest archives into my local github archive repo and generates a permanent link to suit that github repo. We definitely need an automated solution as this is a really infuriating aspect of trying to make code relying on R/BioC packages reproducible.
On Thu, Jan 8, 2015 at 11:28 PM, Björn Grüning bjoern.gruening@gmail.com wrote:
Hi Ross,
this is great! Have you seen this notebook?
http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/R/extract...
It tries to do the same thing. Maybe it's also worth to mention? Maybe we can enhance it?
Thanks, Bjoern
Am 08.01.2015 um 08:09 schrieb Ross:
This may be helpful for anyone else struggling to get complex nested R package dependency installation from the tool shed sorted out. That whole can of worms. While we have setup_r_packages, the developer still has to figure out the right magical incantation and make sure the tarballs are available.
https://wiki.galaxyproject.org/SetUpREnvironment has some notes I've started - contribitions welcome.
It has a more or less reusable R script to generate tool_dependencies.xml boilerplate, assuming you set the constant libdir to your local git repository path where those tarballs will be downloaded from.
I hope this helps someone!
Could make a tool to do this if enough developers want access to it
without
the pain of managing yet another R script?