On 31/03/15 17:41, Martin wrote:
Hi,
I'm trying to install R-3.1.2-goolf-1.5.14.eb.
I'm running a simple:
eb R-3.1.2-goolf-1.5.14.eb --robot -s fetch
but it fails on most of the packages in exts_list. How are people
dealing with this?
this is an issue indeed, bioconductor removes the tarballs of older
versions, I have asked them, and they don't plan to keep old versions
around, since they are considered broken anyway.
I wrote a small script that queries cpan for dependencies and tarball
names/versions to solve the same problem for perl
(https://github.com/JensTimmerman/easybuild-framework/blob/perl_helper/easybuild/scripts/cpan2eb.py
) but there isn't something simliar for bioconductor yet, this could
prove helpful if a lot of people are solving the same issue
Are you just going thru the list and manually fix the versions, I keep
thinking there has to be a better way.
EasyBuild has an option
-k, --skip Skip existing software (useful for installing
additional packages) (def False)
if you combine this with --force
you can first build R without any 'extensions', then change the
exts_lists, and run it with `--force -k`
EasyBuild will then install the R packages inside the already present R
install, if something goes wrong, it will stop at the last installed
package, but the previous succesful installs will be available.
Also how do you (later) install an additional package? Extend the list
in exts_list and "reinstall" or provide another module? Are there
established best practices for this?
thanks,
Martin
Regards,
Jens Timmerman
