[R] regression tests still fail for R version 2.10.0

Gavin Simpson gavin.simpson at ucl.ac.uk
Mon Dec 7 14:10:18 CET 2009 

Do you have R_LIBS set to you library of packages? I got this error
without fail when trying to R CMD check on my hand compiled R
2.10-patched. R_LIBS was set to my own library and it was full of 2.9.x
packages. When I looked in ./tests/reg-tests-1.Rout I got the error
about out of date packages or similar.

It would be useful to see the output from

tail -n 20 ./tests/reg-tests-1.Rout

to see what the problem is. Did you look there?

HTH

G

On Sun, 2009-12-06 at 19:44 +0000, Oliver Kullmann wrote:
> On Sat, Dec 05, 2009 at 01:39:03PM -0500, David Winsemius wrote:
> > The question lacks so many specifics that would be needed to address  
> > problem that I suspect persons with sufficient knowledge to address it  
> > (and I am probably not among that group) simply passed it over and  
> > waited for you to get sufficiently motivated to actually  read the  
> > Posting Guide.
> 
> Thanks for your answer!
> 
> I'm for quite some time now on that mailing list, and I read quite a few
> of the e-mails: Most of the e-mails are far worse, but get quite a lot
> of attention. I can't find anything in the posting guidelines which
> speakes about installation; I also can't find something on what are
> "OS specifics", and how to obtain them from R. There is this session-info,
> which as described seems to be not applicable here, but on the other
> hand seems to be the only thing which yields some output:
> 
> > sessionInfo()
> R version 2.9.2 (2009-08-24)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> This is of course the old version (where the regression tests didn't fail).
> What else could be relevant? Linux was already mentioned (Suse 10.0), 64-bit AMD machine.
> 
> Installation by "./configure --prefix=/path_to_local_directory; make; make check".
> 
> > gcc --version
> gcc (GCC) 4.1.2
> Copyright (C) 2006 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> 
> I'm not aware that there are different source-packages of R around? Other than
> R-2.10.0.tar.gz.
> 
> > md5sum R-2.10.0.tar.gz
> 4486934883b1dbcd5400135e22b26a75  R-2.10.0.tar.gz
> 
> 
> Why I am building from sources? Shouldn't this be irrelevant --- in my
> e-mail I just try to *help* R, and any information on problems should be
> relevant, irrespective of the person who submits such information?
> Anyway, I am redistributing R in a open-source package which provides a kind of
> "complete" environment for some form of scientific investigations; not
> unlike Sage in some sense. See
> http://www.ok-sat-library.org/
> As such I feel responsible to install only software which is correct (and
> I need to install from sources).
> 
> Hope this helps a bit --- feel free to ask!
> 
> Oliver
> 
> 
> 
> > Among the missing items are OS specifics, why you need  
> > to install from sources, which version of the source bundle, (perhaps)  
> > which mirror, etc, etc.
> > 
> > (I surely would not report a bug with so much missing information.)
> > 
> > -- 
> > David.
> > On Dec 5, 2009, at 1:25 PM, Oliver Kullmann wrote:
> > 
> > >Hello,
> > >
> > >on Mon Nov 9 17:57:04 CET 2009 I've sent
> > >an e-mail to the R mailing list (see below),
> > >about a failing regression test. Yet nobody
> > >replied, while (obviously) the situation didn't
> > >change (installation still fails, and might
> > >continue to do so in the future).
> > >
> > >I wonder whether somebody has to say something here?
> > >Shall a bug report be submitted?
> > >Or will R 2.10.1 have fixed the bug?
> > >
> > >Oliver
> > >
> > >--------------------------------------
> > >
> > >Hello,
> > >
> > >I have installed R version 2.9.2, and everything
> > >works fine, but when attempting to install version 2.10.0
> > >I get:
> > >
> > >running code in 'datasets.R' ... OK
> > >comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
> > >make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >running regression tests ...
> > >make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout]  
> > >Error 1
> > >make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >make[3]: *** [test-Reg] Error 2
> > >make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >make[2]: *** [test-all-basics] Error 1
> > >make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests'
> > >make[1]: *** [check] Error 2
> > >make[1]: Leaving directory `/home/csoliver/SAT-Algorithmen/ 
> > >OKplatform/ExternalSources/builds/R/R-2.10.0'
> > >make: *** [R_base] Error 1
> > >
> > >Before that the build seems alright.
> > >
> > >Oliver
> > >
> > >-- 
> > >Dr. Oliver Kullmann
> > >Computer Science Department
> > >Swansea University
> > >Faraday Building, Singleton Park
> > >Swansea SA2 8PP, UK
> > >http://cs.swan.ac.uk/~csoliver/
> > >
> > >______________________________________________
> > >R-help at r-project.org mailing list
> > >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.
> > 
> > David Winsemius, MD
> > Heritage Laboratories
> > West Hartford, CT
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
-- 
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 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
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