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
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
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.gruen...@gmail.com>
> Hi Ross,
> this is great!
> Have you seen this notebook?
> It tries to do the same thing. Maybe it's also worth to mention? Maybe
> we can enhance it?
> 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
> > the pain of managing yet another R script?
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