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

[Joerg Kirschner]

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 <mtmorgan at 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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>>
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>>
>
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