Hi Ross,

you are absolutely right.
My download_store repository is exactly for this purpose.


If you are interested we could integrate your additional magic into the


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.gruen...@gmail.com>
> wrote:
>> Hi Ross,
>> this is great!
>> Have you seen this notebook?
>> http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/R/extract_all_dependencies_from_an_r_package.ipynb
>> 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?
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