Joerg Kirschner
2015-Aug-01 05:48 UTC
[R] Error when compiling R-2.5.1 / *** [d-p-q-r-tests.Rout] Fehler 1
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) 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]]
Martin Morgan
2015-Aug-01 18:16 UTC
[R] Error when compiling R-2.5.1 / *** [d-p-q-r-tests.Rout] Fehler 1
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 at 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
Joerg Kirschner
2015-Aug-02 09:44 UTC
[R] Error when compiling R-2.5.1 / *** [d-p-q-r-tests.Rout] Fehler 1
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 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at 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]]