mmokrejs | 1 Nov 18:17 2004
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[Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

Hi,
  the install script should make sure user has set R_HOME variable.
I don't have it as root, and get stupid messages. Anyway, should it be set
to $blah/R-2.0.0/lib/R/ or $blah/R-2.0.0 ?
Thanks for help
Martin

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Peter Dalgaard | 1 Nov 18:48 2004
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Re: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

mmokrejs <at> ribosome.natur.cuni.cz writes:

> Hi,
>   the install script should make sure user has set R_HOME variable.
> I don't have it as root, and get stupid messages. Anyway, should it be set
> to $blah/R-2.0.0/lib/R/ or $blah/R-2.0.0 ?
> Thanks for help
> Martin

Please read the R-admin manual. The correct way of calling the INSTALL
script is via

   R CMD INSTALL ...

And that will set automatically set R_HOME appropriately.

And please try to avoid reporting your own errors as bugs in R...

--

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard <at> biostat.ku.dk)             FAX: (+45) 35327907

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Prof Brian Ripley | 1 Nov 18:49 2004
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Re: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

On Mon, 1 Nov 2004 mmokrejs <at> ribosome.natur.cuni.cz wrote:

>   the install script should make sure user has set R_HOME variable.

If you mean, R_HOME/bin/INSTALL, that is not an `install script'. It is
documented to be run as R CMD INSTALL, and R (a shell script) sets R_HOME.  
Please see, e.g. `An Introduction to R', ?INSTALL, the `R Installation and
Administration Manual'.  Or even look at the file, which says

usage="Usage: R CMD INSTALL [options] pkgs

> I don't have it as root, and get stupid messages. Anyway, should it be set
> to $blah/R-2.0.0/lib/R/ or $blah/R-2.0.0 ?
> Thanks for help

Please do as we ask and help us by

- reading the posting guide
- reading the relevant documentation
- reading the FAQ on BUGS

before submitting a report.  The second is likely to help you too.

--

-- 
Brian D. Ripley,                  ripley <at> stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

(Continue reading)

Luke Tierney | 1 Nov 19:31 2004
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Re: [Rd] Destructive str(...)?

On Sun, 31 Oct 2004, Prof Brian Ripley wrote:

> Just to be 100% clear, the finalizer is called *at most* once if (as in
> tcltk) R_RegisterCFinalizer is called.  If you want it to be called
> exactly once, you need to use R_RegisterCFinalizerEx.
> 
> The issue is that there may not be a final gc().
> 
> BTW, str(x) is destructive here too, so we do need to improve str().
> I have code written, but access to svn.r-project.org is down (yet again).
> 
> > x <- as.tclObj(pi)
> > str(x)
> Class 'tclObj' length 1 <pointer: 0x860c3f8>
> > str(x)
> length 1 <pointer: 0x860c3f8>
> 

Improving str is a good idea, but as there are other uses of unclass
out there it would probably be best to change the implementation to
wrap the pointers rather than use them directly.

In hindsight it would probably have been better to use an
implementation that internally wraps esxernal pointers as well as
environments so only the bits that really do need reference behavior
get it, and maybe at some point we should consider doing that.  Name
objects should probably just disallow changing attributes as null
currently does.

luke
(Continue reading)

Prof Brian Ripley | 1 Nov 19:50 2004
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Re: [Rd] (PR#7326)(inappropriate) manipulation of expression objects causes segfault (PR#7326)


On 29 Oct 2004, Peter Dalgaard wrote:

> deepayan <at> stat.wisc.edu writes:
> 
> > > foo <- expression(alpha, beta, gamma)
> > > foo[2]
> > expression(beta)
> > > foo[2] <- NA
> > > foo ## or str(foo)
> > Segmentation fault
> > 
> > (Same behaviour in R 1.9.1)
> > 
> > 'foo[[2]] <- NA' works fine, though.
> 
> Right. The NA is not important; foo[2] <- 1 crashes R just as
> effectively. We should likely either give an error or demote [ to [[.
> The latter is what happens with lists, and expressions are basically
> just list of call objects (or names or constants). To wit:
> 
> > x <- list(1,2,3)
> > x[2] <- 1
> > x
> [[1]]
> [1] 1
> 
> [[2]]
> [1] 1
> 
(Continue reading)

ripley | 1 Nov 19:50 2004
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Re: [Rd] (PR#7326)(inappropriate) manipulation of expression objects


On 29 Oct 2004, Peter Dalgaard wrote:

> deepayan <at> stat.wisc.edu writes:
> 
> > > foo <- expression(alpha, beta, gamma)
> > > foo[2]
> > expression(beta)
> > > foo[2] <- NA
> > > foo ## or str(foo)
> > Segmentation fault
> > 
> > (Same behaviour in R 1.9.1)
> > 
> > 'foo[[2]] <- NA' works fine, though.
> 
> Right. The NA is not important; foo[2] <- 1 crashes R just as
> effectively. We should likely either give an error or demote [ to [[.
> The latter is what happens with lists, and expressions are basically
> just list of call objects (or names or constants). To wit:
> 
> > x <- list(1,2,3)
> > x[2] <- 1
> > x
> [[1]]
> [1] 1
> 
> [[2]]
> [1] 1
> 
(Continue reading)

Martin MOKREJŠ | 1 Nov 19:54 2004
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Re: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

Dear all,
 I tried to follow http://www.bioconductor.org/faq.html#getBioC to install it,
and that's why I got to the problem.

Using getBioC to obtain Bioconductor packages

         1. From your R session, type:
            source("http://www.bioconductor.org/getBioC.R")
            this will download the getBioC functionality into your R session.
         2. To install Bioconductor packages, use the function "getBioC" as follows. To download and install the
default packages, type:
            getBioC()
            For a different subset of packages, use the following  values for the libName argument (or "all" for all packages)
                o "all" - gets all packages (warning: This is a very large set)
                o "affy" - gets packages affy, affycomp, affydata, affyPLM, annaffy, gcrma, makecdfenv, matchprobes,
plus "exprs".
                o "cdna" - gets packages marray, vsn, plus "exprs".
                o "default" - gets all packages from "affy", "cdna" and "exprs"
                o "exprs" - gets packages Biobase, annotate, edd, genefilter, geneploter, globaltest,ROC, MAGEML,
multtest, limma, pamr, siggenes and vsn.
                o "graph" - gets packages graph, Rgraphviz and RBGL
                o "prog" - gets packages externalVector, graph, hexbin and Ruuid.
                o "widgets" - gets packages tkWidgets, widgetTools and DynDoc.
                o "database"- gets packages AnnBuilder, SAGElyzer, Rdbi, and RdbiPgSQL.
                o "design" - gets packages daMA and factDesign.
                o "annotation" - gets packages annotate, AnnBuilder, humanLLMappings, KEGG, GO, SNPtools, makecdfenv,
and ontoTools.
                o "analyses" - gets packages Biobase, ctc, daMA, edd, factDesign, genefilter, geneplotter, globaltest,
gpls, limma, RMAGEML, multtest, pamr, ROC, siggenes, and splicegear.
                o "externalData" - gets packages externalVector and rhdf5.
(Continue reading)

James W. MacDonald | 1 Nov 20:15 2004
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Re: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

Martin MOKREJŠ wrote:
> Dear all,
> I tried to follow http://www.bioconductor.org/faq.html#getBioC to 
> install it,
> and that's why I got to the problem.
  You got into a problem because you missed the part where it explains 
that R-2.0.0 currently requires you to install the development versions 
of Bioconductor. Simply replace getBioC() with getBioC(develOK=TRUE).

In addition, questions about BioC packages should really be directed to 
the BioC listserv rather than an R-specific list like R-devel.

HTH,

Jim

--

-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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Uwe Ligges | 1 Nov 20:19 2004
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Re: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)

Martin MOKREJŠ wrote:

> Dear all,
> I tried to follow http://www.bioconductor.org/faq.html#getBioC to 
> install it,
> and that's why I got to the problem.
> 
> 
> Using getBioC to obtain Bioconductor packages
> 
>         1. From your R session, type:
>            source("http://www.bioconductor.org/getBioC.R")

[SNIP]

> Maybe, there are items 3-5 lost. The document doesnt even say how to 
> close R.
> I doubt thise section is NOT for newbies, this describes how to get the 
> things installed,
> right? ;-)
> 
> So, typing "quit" at the ">" prompt doesn't help, btw. ^d is better, the 
> only problem
> is I've no idea if I should say y or n tot he question if I want to save 
> my temporary image ....
> 
> 
> 
> 
> To the INSTALL script actually I got via this problem:
(Continue reading)

tavery | 1 Nov 21:46 2004
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[Rd] ks.test calculations incorrect (PR#7330)

Full_Name: t. avery
Version: 2.0.0
OS: windows xp / Linux
Submission from: (NULL) (131.162.134.159)

ks.test does not produce the correct output.
If given the script:

d1 <- c(53.63984674,0.383141762,1.915708812,0.383141762,10.72796935,6.896551724,20.30651341,5.747126437,0)
d1

d2 <- c(76.43312102,15.2866242,3.821656051,1.27388535,0,0.636942675,1.27388535,0.636942675,0.636942675)
d2

ks.test(d1,d2,alternative="two.sided",exact)

The output generates:
        Two-sample Kolmogorov-Smirnov test

data:  dd and ddd 
D = 0.3333, p-value = 0.6994
alternative hypothesis: two.sided 

Warning message: 
cannot compute correct p-values with ties in: ks.test(dd, ddd, alternative =
"two.sided", exact)

Which is far from the correct D value of:

D = 0.404934475 with a p-value < 0.01
(Continue reading)


Gmane