Dear Martin,
thanks for the advice, I'll check out Bioconductor.
Meanwhile I reinstalled Ubuntu, this time as 64-bit and the error is gone :
)
Rgds, Joerg
On Sat, Aug 1, 2015 at 8:16 PM, Martin Morgan mtmor...@fredhutch.org
wrote:
On 07/31/2015 10:48 PM, Joerg Kirschner wrote:
Hi everyone,
I am new to Linux and R - but I managed to build R-2.5.1 from source to
use
it in Genepattern. Genepattern does only support R-2.5.1 which I could not
find anywhere for installation via apt-get or in the Ubuntu
Software-Centre
(I am using Ubuntu 14.04 (Trusty Tahr) 32-bit)
Are you sure you want to do this? R 2.5.1 is from 2007, which is a very
long time ago. It seems like GenePattern is not restricted to R-2.5.1,
http://www.broadinstitute.org/cancer/software/genepattern/administrators-guide#using-different-versions-of-r
and if their default distribution uses it, then I'm not sure I'd recommend
using GenePattern for new analysis! (Maybe you're trying to re-do a
previous analysis?)
Since GenePattern modules that use R typically wrap individual CRAN or
Bioconductor (http://bioconductor.org) packages, maybe you can take out
the middleman ?
Martin Morgan
But after doing
make check
I get
comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ...make[3]: *** [d-p-q-r-tests.Rout]
Fehler 1
make[3]: Verzeichnis »/home/karin/Downloads/R-2.5.1/tests« wird verlassen
make[2]: *** [test-Specific] Fehler 2
make[2]: Verzeichnis »/home/karin/Downloads/R-2.5.1/tests« wird verlassen
make[1]: *** [test-all-basics] Fehler 1
make[1]: Verzeichnis »/home/karin/Downloads/R-2.5.1/tests« wird verlassen
make: *** [check] Fehler 2
but I can make install and use R for simple plots etc. afterwards - still
I
am worried something is wrong, can you give some advice.
A closer look at the error gives
## PR#7099 : pf() with large df1 or df2:
nu - 2^seq(25,34, 0.5)
y - 1e9*(pf(1,1,nu) - 0.68268949)
stopifnot(All.eq(pf(1,1,Inf), 0.68268949213708596),
+ diff(y) 0, # i.e. pf(1,1, *) is monotone increasing
+ All.eq(y [1], -5.07420372386491),
+ All.eq(y[19], 2.12300110824515))
Error: All.eq(y[1], -5.07420372386491) is not TRUE
Execution halted
As I understand so far some errors are critical some are not - can you
please give some advice on the error above? Can I still use R installed
with that error? What do I need to solve the error?
Thanks, Joerg
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