[R] Error when compiling R-2.5.1 / *** [d-p-q-r-tests.Rout] Fehler 1

[Martin Morgan]

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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>
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