Hi all,
I just came about revoultionary R, which takes a CRAN snapshot for every
release they do,
this could provide us with a lot more stability in the packages if we
follow these repository snapshots.
http://mran.revolutionanalytics.com/documents/rro/reproducibility/#reproducibility
Regards,
Jens Timmerman
On 31/03/15 18:26, Martin wrote:
How about getting rid of of versions (at least for Bioconductor) and
just let R itself deal with it. I find that
"BiocInstaller::biocLite(....)" does work quite nicely. Be it an
upstream mirror or a site local mirror, with a site local mirror the
set of packages is under the local of the the site and there's no need
to remove them during a mirror sync so one would at least have some
kind of archive...
Of course that may then introduce other things like: "Is there a smart
way to set an Rprofile.site from within an easyconfig?" (Yes I'm being
greedy, EB in general works well enough for me to worry about these
Luxury problems)
/Martin
On Tue, Mar 31, 2015 at 6:15 PM Martin <[email protected]
<mailto:[email protected]>> wrote:
Hi,
Yes I know about -k it just seems so cumbersome to do that :(
The combination of a broken corporate proxy and files that go
missing really makes this a mess (for me, EB itself is great, I
just have to suffer the slow Enterprise Death).
I'll look into the script, thanks.
Martin
On Tue, Mar 31, 2015 at 5:58 PM Pablo Escobar Lopez
<[email protected]
<mailto:[email protected]>> wrote:
Hi Martin,
R extensions change quite often and the url also changes so
the normal approach is "manual fix". In case it's useful for
you I wrote this script some days ago to deal with this, it's
not perfect and still requires some manual work but it works
for ~90% of the R libraries so it saves you some time
https://github.com/pescobar/random-scripts/blob/master/easybuild-update-R-libs.py
To install extra R libraries you can just add the new library
to the exts_list and then rerun the easyconfig with "eb
R-3.1.2.eb -k -f" This way only libraries not already
installed will be compiled. This is commonly used to add extra
libraries for R/Perl/Python. This is the easybuild help:
-k, --skip Skip existing software (useful for
installing
additional packages) (def False)
regards,
pablo.
2015-03-31 17:41 GMT+02:00 Martin <[email protected]
<mailto:[email protected]>>:
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?
Are you just going thru the list and manually fix the
versions, I keep thinking there has to be a better way.
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
--
Pablo Escobar López
HPC systems engineer
Biozentrum, University of Basel
Swiss Institute of Bioinformatics SIB
Email: [email protected]
<mailto:[email protected]>
Phone: +41 61 267 21 80
http://www.biozentrum.unibas.ch
