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 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
