[R] Fritz Leisch 1968-2024

[Martyn Plummer]

We are deeply saddened to announce that our friend and colleague Friedrich
(Fritz) Leisch has died.

Fritz obtained his Masters and Doctorate from the Vienna University of
Technology (TU Wien). In 1994, he joined the Department of Statistics and
Probability Theory at TU Wien as an assistant professor. He moved to the
University of Munich (LMU  München) in 2006 as a professor for
Computational Statistics in the Institute of Statistics, becoming head of
department in 2010. He returned to Vienna in 2011 to join the University of
Natural Resources and Life Sciences (BOKU) as head of the Institute of
Applied Statistics and Computing.

Fritz’s contributions to statistical computing began in the early days of
the R project when he was a pioneer of many important innovations. He was
among the first developers who joined Ross Ihaka and Robert Gentleman to
form the R Core Development Team in 1997. He co-founded the Comprehensive R
Archive Network (CRAN) with Kurt Hornik, and developed much of the R
package management system. He was a founding member of the editorial board
of R News, which later evolved into The R Journal, and was the first
Secretary General of the R Foundation for Statistical Computing when it was
formed in 2003. Together with Kurt Hornik, Fritz organized the inaugural
workshop on “Distributed Statistical Computing” (DSC) in Vienna in March
1999, which brought the R Core Team together for its first face-to-face
meeting. Two further DSC conferences were held in 2001 and 2003, followed
by the first useR! conference in 2004. These meetings did much to make
Vienna the spiritual home of R.

Fritz was the first to apply literate programming concepts to the R
language by developing the Sweave system that combines R and LaTeX in a
single document. This introduced reproducible research to the R language
and allowed the first package vignettes to be created, greatly enhancing
the quality of R package documentation.

In addition to his contributions to the R project, Fritz’s research
interests covered many areas including statistical computing, market
segmentation, biostatistics, econometrics, classification, cluster
analysis, time series analysis, software development and statistical
applications in economics, management science and biomedical research. He
taught generations of students at bachelor, master, and PhD level and
introduced hundreds of useRs to proper R development in his "Introduction
to R  Programming" short course.

The R Core Team and the R community at large will miss a contributor,
collaborator, teacher, colleague, and friend.

Martyn Plummer
on behalf of the R Foundation

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[R] Call for proposals to host useR! 2021

[Martyn Plummer]

A call for proposals to host useR! 2021 has been published on the R project
web site:

https://www.r-project.org/useR-2021_call.html

For reasons of sustainability and accessibility we are looking to develop a
distributed conference model with one venue hosting the main useR!
conference and “useR! hubs” running in parallel on other continents. This
call is for groups wishing to host the main venue. We welcome hosts that
are keen to cooperate with us in shaping and developing the new hub model.

The deadline for submitting an outline proposal is *Friday 01 November 2019*
.
On behalf of the R Foundation
Martyn Plummer

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[R] Help wanted - R contributed documentation

[Martyn Plummer]

The R Foundation is looking for a volunteer to organize the collection
of contributed documentation for the R project.  The collection is
currently hosted on CRAN at https://cran.r-project.org/other-docs.html
We want to move it off the CRAN web site.

We think that this task would be suitable for someone whose primary
interest is in library and information science. Ideally the collection
would be reorganized as an R-project.org epub archive, based on re-
using available open source software which features the following: 

* export to .bib
* support for multiple revisions
* support for supplementary material (such as code and data).

If you are interested then please reply privately to me. The R
Foundation board will discuss this at the next meeting.  You can, of
course, put together a team of people but we really want a single
person to act as point of reference.

Martyn Plummer
Co-president, The R Foundation






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[R] Five new ordinary members of the R Foundation

[Martyn Plummer]

The R Foundation has elected five new ordinary members in recognition
of their contributions to the R project:

* Jennifer Bryan 
  https://www.stat.ubc.ca/~jenny/
* Diane Cook 
  http://dicook.github.io/
* Julie Josse 
  http://juliejosse.com/
* Tomas Kalibera
  https://github.com/kalibera 
* Balasubramanian Narasimhan
  https://statistics.stanford.edu/people/balasubramanian-narasimhan

On behalf of the R Foundation I would like to extent my congratulations
and a warm welcome to the new members.

Martyn Plummer
Co-president, The R Foundation
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[R] New R logo

[Martyn Plummer]

The R logo has been revised in to be more compatible with the principles
of flat design followed by some recent user interfaces such as Microsoft
Windows >= 8 and Mac OS X >= 10.10 (Yosemite). The new logo is
available for download from the R project web site in SVG and
high-resolution PNG formats:

https://www.r-project.org/logo

Thanks to Hadley Wickham and others at RStudio for lending their graphic
design skills.

The logo is dual licensed. You may use either the Creative Commons
Attribution-ShareAlike 4.0 International license (CC-BY-SA 4.0) or the
GNU General Public License version 2 (GPL‑2). For further details,
please refer to the link above.

For the R Foundation
Martyn Plummer, Co-President

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Re: [R] rjags cannot find JAGS-4.0.0

[Martyn Plummer]

On Fri, 2015-11-27 at 11:27 -0800, David Winsemius wrote:
> > On Nov 26, 2015, at 4:59 PM, Margaret Donald  
> > wrote:
> > 
> > 1. Despite being in R with administrative rights  the library "rjags" loads
> > in a temporary location.
> > 
> >> install.packages("rjags", dependencies=TRUE,
> > +   lib= "C:/Users/Margaret Donald/Documents/R/win-library/3.2")
> > trying URL 'https://cran.r-project.org/bin/windows/contrib/3.2/rjags_4-4.zip
> > '
> > Content type 'application/zip' length 525871 bytes (513 KB)
> > downloaded 513 KB
> > 
> > package ‘rjags’ successfully unpacked and MD5 sums checked
> > 
> > The downloaded binary packages are in
> >C:\Users\Margaret
> > Donald\AppData\Local\Temp\RtmpMzv76s\downloaded_packages
> 
> That’s not an indication of an error. The installation process always does 
> that.
> 
> 
> > #-
> > 
> > 2. Cannot find JAGS-4.0.0 which is in C;\programs\JAGS\JAGS-4.0.0.  How do
> > I get R to see JAGS-4.0.0

The Windows installer writes some keys in the Windows registry. These
keys are then read by the rjags package when it is loaded to locate the
JAGS DLL.

I don't know why this is not working in your case. You might try
uninstalling and reinstalling JAGS (and by this I mean that the user who
installed it should uninstall it from the Control Panel).

Otherwise, as David says, you can set the environment variable
JAGS_HOME. Note that if you previously set JAGS_HOME in .Rprofile and
have upgraded to a new version of JAGS, then JAGS_HOME will be pointing
to the wrong place. This might explain why rjags cannot find JAGS and
this is why I do not recommend this solution except as a last resort.

> You might try to use Sys.setenv to create a properly directed JAGS_HOME
> 
> Sys.setenv(JAGS_HOME=“C:\programs\JAGS\JAGS-4.0.0”)
> 
> (I corrected the semi-colon.) 
> >> library(rjags)
> > Error : .onLoad failed in loadNamespace() for 'rjags', details:
> >  call: fun(libname, pkgname)
> >  error: Failed to locate any version of JAGS version 4
> > 
> > The rjags package is just an interface to the JAGS library
> > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> > http://www.sourceforge.net/projects/mcmc-jags/files
> 
> I’m was having a perhaps similar problem on a Mac. The binary version
> 3-15 of rjags installed today from CRAN was trying to
> access /usr/local/lib/libjags.3.dylib, but since I have installed JAGS
> version 4.0.1 installed from the SourceForge repository, there is no
> ligjags.3.dylib, but instead there was only
> a /usr/local/lib/libjags.4.dylib

rjags_4-4 requires JAGS 4.x.y and the previous version rjags_3-15 is not
compatible with JAGS 4.0.0. Unfortunately the Mac OS X binaries on CRAN
are not up to date. I have no control over this but Matt Denwood has
made a binary for Mavericks or later available on Sourceforge:

http://sourceforge.net/projects/mcmc-jags/files/rjags/4/rjags_4-4.tgz

Martyn

> Going back to SourceForge and tracking down the older version of JAGS
> and installing version 3.4.0 was successful in getting rjags to load
> correctly. I suspect that with the release of JAGS v4 that there is
> some mismatch among the various editions of rjags and JAGS.
> 
> — 
> David
> > 
> > Error: package or namespace load failed for ‘rjags’
> >> library(R2jags)
> > Loading required package: rjags
> > Error : .onLoad failed in loadNamespace() for 'rjags', details:
> >  call: fun(libname, pkgname)
> >  error: Failed to locate any version of JAGS version 4
> > 
> > The rjags package is just an interface to the JAGS library
> > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> > http://www.sourceforge.net/projects/mcmc-jags/files
> > 
> > Error: package ‘rjags’ could not be loaded
> >> 
> > 
> > Regards,
> > Margaret Donald
> > -- 
> > Margaret Donald
> > Post Doctoral researcher
> > University of New South Wales
> > margaret.don...@unsw.edu.au
> > 0405 834 550
> > 
> > [[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.
> 
> David Winsemius
> Alameda, CA, USA
> 

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[R] Codes of Conduct at R Conferences

[Martyn Plummer]

The useR! conferences in 2014 and 2015 both had codes of conduct in
order to ensure an experience free from harassment for all participants.
After a request from some members of the R community, the R Foundation
has decided to endorse this practice. Future conferences supported by
the R Foundation must have a code of conduct.  We encourage other R
meetings not affiliated with the R Foundation to adopt the same policy.

A code of conduct serves two important purposes. Firstly, it sends a
clear message to those outside the community that an R conference is a
professional and comfortable working environment for all participants.
Secondly, it provides a mechanism for reporting and monitoring any
incidents of harassment that may occur.

We have decided not to require a particular formulation for the code of
conduct, but suggest that conference organizers use the model of the
useR! 2015 meeting ( http://user2015.math.aau.dk/behaviouR ). This will
allow the code to be adapted to local circumstances and to evolve in the
future. Conference organizers should ensure that any sanctions laid out
in the code of conduct are legally and practically enforceable. 

Vigorous debate and lively exchange are important features of R
conferences. We expect this to continue within the boundaries set by the
code of conduct.

For the R Foundation
Martyn Plummer, Co-President

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[R] The R Journal, Volume 4, Issue 2

[Martyn Plummer]

Dear All,

The latest issue of The R Journal is now available
at http://journal.r-project.org/current.html

Thanks to everyone involved.

Martyn Plummer
Editor-in-Chief

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[R] The R Journal, Vol. 4 Issue 1

[Martyn Plummer]

Dear All,

The first issue of the fourth volume of The R Journal is now available
at http://journal.r-project.org/current.html

Thanks to everyone involved.

Martyn Plummer
Editor-in-Chief


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Re: [R] rjags installation trouble

[Martyn Plummer]

It looks like you are cross-linking to an earlier version of the JAGS
library at run time. Check

/sbin/ldconfig -p | grep jags -

When compiling rjags, you can hard-code the location of the jags library
using the [GNU-specific] configure option --enable-rpath.

Martyn

On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote:
 Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0
 installed on Ubuntu 10.04, with r-devel ... the bottom line is that it
 fails while loading with
 
  /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb
 
   Has anyone else seen this or is it a glitch somewhere in my system?
 
   thanks
 Ben Bolker
 
 ==
 bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags
 Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012
 JAGS is free software and comes with ABSOLUTELY NO WARRANTY
 Loading module: basemod: ok
 Loading module: bugs: ok
 .
 
 ===
 
 install.packages(rjags) starts out fine:
 
 Installing package(s) into
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’
 (as ‘lib’ is unspecified)
 trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz'
 Content type 'application/x-gzip' length 66429 bytes (64 Kb)
 opened URL
 ==
 downloaded 64 Kb
 
 * installing *source* package ‘rjags’ ...
 ** package ‘rjags’ successfully unpacked and MD5 sums checked
 checking for prefix by checking for jags... /usr/bin/jags
 
   [snip snip]
 
 ** libs
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c jags.cc -o jags.o
 g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
 -I/usr/local/include-fpic  -g -O2  -c parallel.cc -o parallel.o
 g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags
 installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs
 ** R
 
   [snip snip]
 
   but fails at:
 
 ** building package indices
 Error : .onLoad failed in loadNamespace() for 'rjags', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object
 '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so':
 
 /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so:
 undefined symbol: _ZN7Console15checkAdaptationERb
 ERROR: installing package indices failed
 * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
 * restoring previous
 ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
 
 The downloaded source packages are in
   ‘/tmp/RtmpSKHIz5/downloaded_packages’
 Warning message:
 In install.packages(rjags) :
   installation of package ‘rjags’ had non-zero exit status
  sessionInfo()
 R Under development (unstable) (2012-01-01 r58032)
 Platform: i686-pc-linux-gnu (32-bit)
 
 locale:
  [1] LC_CTYPE=en_CA.utf8   LC_NUMERIC=C
  [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8
  [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8
  [7] LC_PAPER=CLC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C
 
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 
 loaded via a namespace (and not attached):
 [1] tools_2.15.0


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Re: [R] cacheSweave fails when used in conjunction with rjags

[Martyn Plummer]

Hi Roger,

If you do not supply an explicit data list, the jags.model() function
will try to get the data from the calling environment.  This is
obviously not working with cacheSweave, but if you do supply an explicit
list, like this:

m - jags.model(j.bug, data=list(y=y))

it will work.

Martyn


On Thu, 2010-03-25 at 22:57 -0700, Roger Levy wrote:
 Hi all,
 
 I use the excellent packages rjags and cacheSweave, and unfortunately  
 seem to have found an incompatibility between them.  Below are a  
 minimal .Rnw file and corresponding JAGS model file which illustrate  
 the problem:
 
 *** JAGS model file; name=j.bug ***
 model {
mu ~ dnorm(0,1.0E-5)
sigma ~ dunif(0,100)
for(i in 1:length(y)) {
  y[i] ~ dnorm(mu,sigma)
}
 }
 ***
 
 *** .Rnw file; name=testCacheSweave-jags.Rnw ***
 \documentclass[12pt]{article}
 \usepackage{Sweave}
 
 \begin{document}
 
 loadLib=
 library(rjags)
 @
 
 testJags,cache=T=
 y - rnorm(100)
 m - jags.model(j.bug)
 update(m,100)
 res - coda.samples(m,c(mu,sigma),n.iter=1000)
 @
 
 plotResults,fig=T=
 plot(res)
 @
 \end{document}
 ***
 
 
 When I run Sweave with cacheSweaveDriver, I get the following error  
 (note that this happens on the first invocation, not just on repeat  
 invocations):
 
   Sweave(testCacheSweave-jags.Rnw,driver=cacheSweaveDriver)
 Writing to file testCacheSweave-jags.tex
 Processing code chunks ...
   1 : echo term verbatim (label=loadLib)
   2 : echo term verbatim (label=testJags)
 
 Error:  chunk 2 (label=testJags)
 Error in jags.model(j.bug) : RUNTIME ERROR:
 Unable to evaluate upper index of counter i
 
 
 Reading through the cacheSweave documentation, it remains unclear to  
 me why this error would occur.  Would anyone be able to clarify, and/ 
 or suggest a possible workaround?  It's an unfortunate conflict  
 because running JAGS models is one of the most computation-intensive  
 operations that I have in my .Rnw document.
 
 Best  many thanks in advance.
 
 Roger
 
 
 --
 
 Roger Levy  Email: rl...@ling.ucsd.edu
 Assistant Professor Phone: 858-534-7219
 Department of Linguistics   Fax:   858-534-4789
 UC San DiegoWeb:   http://ling.ucsd.edu/~rlevy
 
 
 
 
 
 
 


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Re: [R] Binaries no longer compiled for RH EL4, i386?

[Martyn Plummer]

The maintainer of the RHEL RPMs no longer has an i386 machine running
EL4, and cross-building on an x86_64 machine did not work, so I did not
distribute them.

As noted in a previous thread, there is a project to port the Fedora R
RPMs to Enterprise Linux:

On Thursday 23 April 2009 15:08:26 Marc Schwartz wrote:
 More info here:

http://fedoraproject.org/wiki/EPEL

 and the specific link for R for RHEL 4/x84_64 is:

http://download.fedora.redhat.com/pub/epel/4/x86_64/repoview/R.html

RPMs for R 2.9.0 have been built but not pushed yet.

In the future I will put the EPEL RPMs on CRAN so that they are
compatible with the Fedora RPMs.

Martyn


On Thu, 2009-04-30 at 07:48 -0700, Waichler, Scott R wrote:
 I see that R 2.9.0 *.rpms have been compiled for RH EL5, i386 and
 x86_64, and also for EL4 x86_64, but not for EL4 i386.  Is this an
 oversight or will that version no longer be compiled?
 
 Scott Waichler
 Pacific Northwest National Laboratory
 scott.waich...@pnl.gov
 

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Re: [R] Fedora 10 KDE plasma font rendering issue

[Martyn Plummer]

On Sun, 2009-04-12 at 13:19 +0100, Paul Bivand wrote:
 I checked with my KDE 4.2 (Mandriva 2009 system, kde.org binaries)
 with no font rendering issues in running demo(graphics).
 
 It is quite possible that pango was not installed with Fedora (as it
 is unnecessary for KDE 4.2 systems). Installing the relevant rpm may
 fix things.

The pango RPM should have been installed with R, as R requires the pango
and pangocairo libraries that it provides:

[mar...@seurat ~]$ rpm -q --requires R-core | grep pango -
libpango-1.0.so.0()(64bit)  
libpangocairo-1.0.so.0()(64bit)  

 The packaging of the Fedora 2.8.1 rpm may need to take this into
 account - if compiling, you'd have discovered at configure stage.
 
 Paul Bivand
 
 Paul Bivand
 
 2009/4/1 Martyn Plummer plum...@iarc.fr:
  On Tue, 2009-03-31 at 18:36 -0700, dfermin wrote:
  Nope. I checked this. Both those fonts are installed.
 
  Well it is some kind of font rendering problem. The default device is
  the Cairo X11 device, which uses the Pango layout engine for font
  rendering.
 
  If you set the environment variable FC_DEBUG to 1 before launching your
  R session, you will get some debugging information. It is very verbose,
  but we only need to see this bit:
 
  First font Pattern has 15 elts (size 15)
 family: Nimbus Sans L(w)
 style: Regular(w)
 slant: 0(i)(w)
 weight: 80(i)(w)
 width: 100(i)(w)
 foundry: urw(w)
 file: /usr/share/fonts/default/Type1/n019003l.pfb(w)
 index: 0(i)(w)
 outline: FcTrue(w)
 scalable: FcTrue(w)
 
 
 
 
  Martyn Plummer-2 wrote:
  
   Quoting dfermin dfer...@umich.edu:
  
   Hello.
  
   I've got a new workstation running Fedora 10 linux and I use the KDE 4.2
   desktop which uses some kind of new desktop environment called 'plasma'.
  
   If I start up R and generate a plot (for example: hist(rnorm(1,
   mean=0,
   sd=1), breaks=100) ). The plot appears but all text (the x/y axes, 
   title,
   etc..) is replaced by a square box. No font is rendered at all.
  
   Has anyone else got this problem? If so do you have a work around or a
   solution?
  
   I'm using R version 2.8.1 installed from the Fedora 10 repositories if
   that
   helps.
  
   Thanks in advance.
  
   It sounds like you are missing some fonts. Check that the urw-fonts and
   liberation-fonts RPMs are installed.
 
 
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Re: [R] Which model to keep (negative BIC)

[plummer]

Quoting cladoo.26 cladoo...@laposte.net:
 Hi,

 My questions concern the function 'mclustBIC' which compute BIC for a range
 of clusters of several models on the given data and the other function
 'mclustModel' which choose the best model and the best number of cluster
 accordind to the results of the previous cited function.

 1) When trying the following example (see ?mclustModel), I get negative BIC
 computed by 'mclustBIC', and the best model according to the results of
 'mclustModel' is the one with the highest BIC (i.e. the closer to zero).

 irisBIC - mclustBIC(iris[,-5])
 plot(irisBIC)
 mclustModel(iris[,-5], irisBIC)

 Because I don't find anything about this point, could someone confirm that
 when the BIC are positive, we try to the minimize the criterion (the model
 with the smallest BIC is the best one) but when the BIC are negative we look
 for the higher BIC (the model with a the BIC closest to zero is the best one)
 ?

The mclust package seems to be using a definition of BIC that is the
negative of the usual one, i.e. the bic() function in the mclust package
returns

2 * loglik - nparams * log(n)

where loglik is the log likelihood, n is the number of observations
and nparams is the number of parameters.

BIC is normally defined as

   -2 * loglik + nparams * log(n)

and the optimal model is the one with the minimum BIC. However in this
case, you want to maximize it.


 2) Does the $G argument from the output of  'mclustModel' represent the best
 number of clusters for the chosen model ?

According to the documentation it does, and you can verify from your
plot that the VEV model with 2 components has maximum BIC

 Many thanks, this is my first post on R help, but I often consult the forum
 for 4 years.

 Cladoo




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Re: [R] Fedora 10 KDE plasma font rendering issue

[Martyn Plummer]

On Tue, 2009-03-31 at 18:36 -0700, dfermin wrote:
 Nope. I checked this. Both those fonts are installed.

Well it is some kind of font rendering problem. The default device is
the Cairo X11 device, which uses the Pango layout engine for font
rendering. 

If you set the environment variable FC_DEBUG to 1 before launching your
R session, you will get some debugging information. It is very verbose,
but we only need to see this bit:

First font Pattern has 15 elts (size 15)
family: Nimbus Sans L(w)
style: Regular(w)
slant: 0(i)(w)
weight: 80(i)(w)
width: 100(i)(w)
foundry: urw(w)
file: /usr/share/fonts/default/Type1/n019003l.pfb(w)
index: 0(i)(w)
outline: FcTrue(w)
scalable: FcTrue(w)



 
 Martyn Plummer-2 wrote:
  
  Quoting dfermin dfer...@umich.edu:
 
  Hello.
 
  I've got a new workstation running Fedora 10 linux and I use the KDE 4.2
  desktop which uses some kind of new desktop environment called 'plasma'.
 
  If I start up R and generate a plot (for example: hist(rnorm(1,
  mean=0,
  sd=1), breaks=100) ). The plot appears but all text (the x/y axes, title,
  etc..) is replaced by a square box. No font is rendered at all.
 
  Has anyone else got this problem? If so do you have a work around or a
  solution?
 
  I'm using R version 2.8.1 installed from the Fedora 10 repositories if
  that
  helps.
 
  Thanks in advance.
  
  It sounds like you are missing some fonts. Check that the urw-fonts and
  liberation-fonts RPMs are installed.


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Re: [R] Fedora 10 KDE plasma font rendering issue

[plummer]

Quoting dfermin dfer...@umich.edu:

 Hello.

 I've got a new workstation running Fedora 10 linux and I use the KDE 4.2
 desktop which uses some kind of new desktop environment called 'plasma'.

 If I start up R and generate a plot (for example: hist(rnorm(1, mean=0,
 sd=1), breaks=100) ). The plot appears but all text (the x/y axes, title,
 etc..) is replaced by a square box. No font is rendered at all.

 Has anyone else got this problem? If so do you have a work around or a
 solution?

 I'm using R version 2.8.1 installed from the Fedora 10 repositories if that
 helps.

 Thanks in advance.

It sounds like you are missing some fonts. Check that the urw-fonts and
liberation-fonts RPMs are installed.



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Re: [R] R with MKL

[Martyn Plummer]

Both gcc and MKL are moving targets.  So if you are using a more recent
version of gcc than the one used to compile MKL then you are potentially
in trouble.

In this case, you still have the option of using Intel threads
(libmkl_intel_thread) instead of the GNU thread library. In this case
you must dynamically link to the Intel OpenMP runtime library libiomp5
instead of the GNU library libgomp.

Of course, this does not help if you want to make a portable version of
R, statically linked to MKL.

On Wed, 2009-03-18 at 21:17 +0900, Ei-ji Nakama wrote:
 Hi Cristián.
 
  However, It is a little different.( -lgomp and configure line)
 
  MKL=   -...@{mkl_lib_path@}   \
 -Wl,--start-group   \
 $...@{mkl_lib_path@}/libmkl_gf_lp64.a\
 $...@{mkl_lib_path@}/libmkl_gnu_thread.a \
 $...@{mkl_lib_path@}/libmkl_core.a   \
 -Wl,--end-group \
 -lgomp -lpthread
  ./configure --with-blas=$MKL --with-lapack=$MKL
 
  ...
 
  Thanks for all your answers. I read carefully the userguide and the
  admin guide. I now understand that with gfortran I need to use
  libmkl_gf_lp64 and libmkl_gnu_thread, either shared or static.
  Unfortunately for MKL version 10.1.1.019, libmkl_gnu_thread links
  against the symbol _gfortran_internal_malloc64 which was present in
  gcc-4.1 and is not present anymore in gcc-4.3.
 
 However, the support  of openmp is gcc-4.2 or latter.
 
  So my alternatives are installing an older compiler, waiting for a
  newer MKL version, building R with Intel compiler or switching away
  from MKL.
 
 Please download the following files, and test the procedure to which
 the file is written first.
 
   http://prs.ism.ac.jp/~nakama/mkl/mkl_gf.c
 

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Re: [R] [Rd] R with MKL

[Martyn Plummer]

On Tue, 2009-03-17 at 12:12 +0900, Ei-ji Nakama wrote:
 Hi
 
  I have seen a lot of problems from people trying to compile R with
  MKL. So I am writing my experience in case it helps and to ask one
  question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using
  MKL 10.1.1.019.
 
 Do you use gcc and gfortran?
 
  I configured correctly (following MKL userguide) with :
 
  sudo ./configure --with-blas=-I/opt/intel/mkl/10.1.1.019/include
  -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64
  -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
  --with-lapack=-I/opt/intel/mkl/10.1.1.019/include
  -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64
  -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
 
 cited reference https://svn.r-project.org/R/trunk/doc/manual/R-admin.texi
 | You are strongly encouraged to read the MKL User's Guide
 | snip
 | @example
 | MKL=   -...@{mkl_lib_path@}   \
 | -Wl,--start-group   \
 | $...@{mkl_lib_path@}/libmkl_gf_lp64.a\
 | $...@{mkl_lib_path@}/libmkl_gnu_thread.a \
 | $...@{mkl_lib_path@}/libmkl_core.a   \
 | -Wl,--end-group \
 | -liomp5 -lpthread
 | @end example
 
 However, It is a little different.( -lgomp and configure line)
 
 MKL=   -...@{mkl_lib_path@}   \
 -Wl,--start-group   \
 $...@{mkl_lib_path@}/libmkl_gf_lp64.a\
 $...@{mkl_lib_path@}/libmkl_gnu_thread.a \
 $...@{mkl_lib_path@}/libmkl_core.a   \
 -Wl,--end-group \
 -lgomp -lpthread
 ./configure --with-blas=$MKL --with-lapack=$MKL

Yes I see. If you are statically linking to MKL, you want to link to the
GNU OMP runtime for portability. Sorry about that.

  But in order to compile had to edit src/modules/lapack/vecLibg95c.c
  and comment out the include. Weird, since I am not building for Mac.
 
 Please note the thing that ABI of fortran is different with Intel compiler
 and GNU compiler.
 difficult to detect the mistake.

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Re: [R] R with MKL

[Martyn Plummer]

On Mon, 2009-03-16 at 18:33 -0400, Cristián wrote:
 Hi,
 
 I have seen a lot of problems from people trying to compile R with
 MKL. So I am writing my experience in case it helps and to ask one
 question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using
 MKL 10.1.1.019.

The R-admin manual has been updated with instructions for MKL since the
last thread on the topic. You should look there in section A.3.1.4.
 
 I configured correctly (following MKL userguide) with :
 
 sudo ./configure --with-blas=-I/opt/intel/mkl/10.1.1.019/include
 -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64
 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
 --with-lapack=-I/opt/intel/mkl/10.1.1.019/include
 -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64
 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
 
 But in order to compile had to edit src/modules/lapack/vecLibg95c.c
 and comment out the include. Weird, since I am not building for Mac.

OK. There are two things happening here. 

You are using the wrong interface layer. With gcc you need to use
-lmkl_gf_lp64, since the way that complex numbers are represented
differs between Intel and GNU compilers.

There is a known workaround for this problem for MacOs X, using the
cblas interface.  Apparently, this workaround is also being applied
here.  I will look into it.

 Make check returned no error. I checked with ldd that R is linked
 against MKL. All demos run
 
 I set MKL_NUM_THREADS={1,2} environment var and run R-benchmark-25.R
 from (http://r.research.att.com/benchmarks/R-benchmark-25.R). Not all
 tests use MKL so you get around 20% improvement for 2 cores. Also
 monitoring with top you can see which tests use 2 cores.
 
 Question: Am I set? What was that error relating to vecLib? I need to
 install now on a bigger multicore server for data-mining and dont want
 to deliver a defective installation. Maybe I could run a larger
 check-benchmark.
 
 Thanx a lot,
 
 C.
 
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Re: [R] [Rd] Error: bad value problem

[Martyn Plummer]

This has all the hallmarks of a bug I found and fixed in R-devel
(r46998).  I did not port the patch over to the R release branch because
I could not reproduce the bug.

In R-devel, I was seeing problems with make test-Segfault. This would
occasionally segfault, but most of the time would create the bad value
error, and of course would also run perfectly fine a lot of the time.
The error came from exactly the same place that Ben found.  It was due
to an invalid SrcRefs being used because SrcFile is not set to zero when
it should be.

I'll have a look and see if it is the same problem, or a close cousin.

Martyn


On Wed, 2008-12-17 at 22:07 -0500, Duncan Murdoch wrote:
 On 17/12/2008 9:47 PM, Duncan Murdoch wrote:
  On 17/12/2008 8:56 PM, Peter Dalgaard wrote:
  Ben Bolker wrote:
I can get the errors to happen on Ubuntu 8.10 with R --vanilla 
  (*without*
  valgrind) -- but
  editing momfit.r line 742 so that plot.progress=FALSE seems to make the
  problem go away.  (This was a lucky guess, it looked like there was
  something
  odd going on with the plots.)
 
Hope that helps someone ...
  Probably not. The problem is to reproduce the error state in a way so 
  that we can understand what is causing it.
 
  I can debug this to
  (gdb) bt
  #0  Rf_error (format=0x8220c65 bad value) at 
  ../../../R/src/main/errors.c:704
  #1  0x0805a924 in SETCDR (x=0x8f89348, y=0x9b276e8)
   at ../../../R/src/main/memory.c:2728
  #2  0x0819fa46 in GrowList (l=0x951e8f4, s=value optimized out) at 
  gram.y:958
  #3  0x081a2a7b in xxvalue (v=0x8f89348, k=4, lloc=value optimized out)
   at gram.y:440
 
  and the problem in GrowList is that CAR(l) is R_NilValue (==0x8f89348), 
  which supposedly cannot happen, and the thing that calls GrowList is 
  something with srcrefs (DuncanM?).
 
  Digging deeper probably has to wait till the weekend for my part. (The 
  natural next step is figuring out how the R_NilValue got into that 
  location, but I should try to sleep off this cold)
 
  I'm CCing r-devel on this. Can we move the discussion there?
  
  I can probably take a look tomorrow.  I wasn't getting an error, but 
  maybe I'll see the same corruption if I watch it run.
 
 I had time to see if I was getting a NilValue there tonight, and the 
 answer was no, with the Windows RC.  I don't get the error in any 
 version I've tried on Windows, though I can see it in 2.8.0 on MacOSX.
 
 Duncan
  
  Duncan Murdoch
  
 
 
Ben Bolker
 
  sessionInfo()
  R version 2.8.0 (2008-10-20) 
  i486-pc-linux-gnu 
 
  locale:
  LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
 
  attached base packages:
  [1] stats graphics  grDevices utils datasets  methods   base
 
  
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Re: [R] R crash with dyn.load

[Martyn Plummer]

On Thu, 2008-12-18 at 17:18 +0100, Thibault Helleputte wrote:
 Hello,
 
 I try to incorporate C code in R.
 
 suppose I have the following C code:
 
 #include R.h
 #include stdio.h
 
 int main(int *n)
 {
 int i;
 for(i=0; i  *n; i++) {
 printf(Hello, world!\n);
 }
  }
 
 
 in a file named hello.c. First I make:
 
 g++ -c hello.c -o hello.o -I
 /Library/Frameworks/R.framework/Versions/2.8/Headers/
 g++ -dynamic hello.o -o hello.so
 
 I work on mac, and that's why I have to set the -dynamic option. First
 of all, I don't understand why I have to specify the path to R.h, but if
 I don't, R.h isn't found.
 
 My problem is the following: once the .so is generated, without any
 warning or error, I open my R envirronment and type
 
  dyn.load(/path/to/my/hello.so)
 
 then push on enter, and then R runs  hours, without giving me the
 command invite again. What am I doing wrong?

It might have something to do with the fact that you call your function
main. Try renaming it.

Also have a look at section 5.5 of the Writing R Extensions manual on
creating shared objects for loading into R.

Martyn

 Thank you.

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Re: [R] Problems with graphical devices, e.g., png(), pdf(): blurry graphical output

[Martyn Plummer]

The artefacts that you see are a normal result of using bitmap graphics
devices.  I have tried to explain these below:

I have looked at your figures in Eye of Gnome, with anti-aliasing turned
off (Menu Edit/Preferences; Tab Image View; option Smooth images when
zoomed).  I recommend that you do the same.

 png('test.png',antialias='none') # type is 'cairo'
 plot(1:10)
 dev.off()
 ## result: no fuzziness at all but the box is missing
 ## the top and left border lines
 ## http://www.piccdrop.com/images/1229495388.png

Cairo works in real (double precision) coordinates. But the line must be
converted to bitmap to be displayed. When this is done without
anti-aliasing, it is quite possible for a thin horizontal or vertical
line to pass in-between the points on a grid that are sampled to form
the bitmap image, and hence disappear.

 png('test.png') # type is 'cairo'
 plot(1:10)
 dev.off()
 ## result: box lines fuzzy at top and left, and appears 
 ## darker and thicker where the axes are overplotted
 ## http://www.piccdrop.com/images/1229495327.png

With anti-aliasing, a horizontal or vertical line may appear as a 1
pixel wide black line, but is more likely to appear as a 2 pixel wide
grey line.  When two such grey lines are over-plotted, they will create
a darker grey line. The overplotted line also appears thicker, but this
is an optical illusion.

 png('test.png',type='Xlib')
 plot(1:10)
 dev.off()
 ## result: no fuzziness at all and no lines missing
 ## http://www.piccdrop.com/images/1229495428.png

Xlib works in integer coordinates. When a line is plotted in Xlib, the
start and end coordinates are cast to integer before plotting. Hence
horizontal/vertical lines will always appear, with a width of 1 pixel
and overplotting does not change the appearance of a line.

Martyn

On Wed, 2008-12-17 at 01:36 -0800, Y-H Chen wrote:
 On Wed, Dec 17, 2008 at 12:54 AM, Prof Brian Ripley
 rip...@stats.ox.ac.uk wrote:
  Your PDF problems indicate a broken viewer.  How were you viewing PDF?
 
 You are absolutely correct about the PDF files; I've since checked the
 PDF files in other viewers and have not been able to reproduce the
 problem. There was definitely something wrong with my default viewer.
 I am most certainly embarrassed.
 
 As for the PNG files: I've viewed the PNG files on two different
 systems, in various viewers. On a Fedora system in Eye of Gnome,
 Firefox, Epiphany, GIMP, and gThumb. And, on a Windows system in
 Paint, Firefox, Internet Explorer, and GIMP. I see blurriness in all
 of these viewers for all of the files I originally claimed difficultly
 with (as mentioned in my last message, I don't see blurriness in the
 images produced via type='Xlib'). I'll do more tests on other systems
 once I get the chance, but that's what I see at the moment. The files
 are linked to in the text file I provided, and you are all invited to
 check those out if you are interested.
 
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Re: [R] R2winbugs : vectorization

[plummer]

Philip,

If you are using WinBUGS 1.4, then the poor performance of the
inprod function is a known problem.  An inprod2 function
was introduced in 1.4.3 to improve performance.  See

http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml#problems

You might try using that.

For WinBUGS problems, you should probably try the BUGS mailing
list before this one:

http://www.jiscmail.ac.uk/lists/bugs.html

Martyn

Quoting Ben Bolker bol...@ufl.edu:




 Philip A. Viton wrote:
 
 
  I'm new to bugs, so please bear with me. Can someone tell me if the
  following two models are doing the same thing? The reason I ask is
  that with the same data, the first (based on 4 separate coeffs
  a1--a4) takes about 50 secs, while the second (based on a vectorized
  form, a[]) takes about 300. The means are about the same, though
  R-hat's in the second version are quite a bit better.
 

 The model definitions do seem to be formally equivalent, but BUGS
 is a pretty big-ugly-black-box thing, and your timing (and Rhats)
 seem to be pretty good evidence that WinBUGS is *not* constructing
 the same sampler in both cases.  (Do the posterior distributions agree
 once you get to convergence?)

 You could try the same model in JAGS (the R2jags package lets
 you use the same R code to call it, just substituting jags() for
 bugs() if you wanted to pursue this further. In my limited experience
 JAGS is usually slower than WinBUGS but it's a good cross-check.


 Philip A. Viton wrote:
 
  (Also, and completely unrelated: is there any way to get more than 2
  decimal places in the display of the means?)
 
  [snip snip snip]
 

 print(bugs.object,digits=5)

   Ben Bolker

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 View this message in context:
 http://www.nabble.com/R2winbugs-%3A-vectorization-tp21019193p21021187.html
 Sent from the R help mailing list archive at Nabble.com.

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Re: [R] unable to install rjags on 64-bit Debian Linux (etch)

[plummer]

Quoting Prof Brian Ripley [EMAIL PROTECTED]:

 On Sat, 8 Nov 2008, Roger Levy wrote:

  While I have been able to install rjags on my Windows computer, oddly I
 have
  been unable to install rjags successfully on my 64-bit Linux compute server
  (etch, Linux kernel 2.6.18).  I am required to specify the JAGS module
  directory upon installation; when doing this within R, I get:
 
 

install.packages(rjags,configure.args=--with-jags-modules=/usr/local/lib/JAGS/modules/)
 
  which works fine, but then trying to load rjags gives an error:
 
  library(rjags)
  \Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library
  '/usr/local/lib64/R/library/rjags/libs/rjags.so':
   libjags.so.1: cannot open shared object file: No such file or directory
  Error : .onLoad failed in 'loadNamespace' for 'rjags'
  Error: package/namespace load failed for 'rjags'
 
  I'm not sure how to read this error.  Does anyone have any suggestions?

 It means that ld.so (the runtime linker) cannot find libjags.so.1.

 Where is your libjags.so.1?  My guess is that you installed it into
 /usr/local/lib, since that is what you have for your module path.  On a
 64-bit Linux system it should be in /usr/local/lib64.  (I had to tell the
 JAGS installation that via libdir=/usr/local/lib64 on the configure line.)

Debian conforms to the filesystem hierarchy standard (FHS) which
states that libraries go in prefix/lib and alternative format
binaries go in prefix/libqual.  I would prefer it if everyone
agreed on where 64-bit libraries should go. But they don't.

In the mean time, we have to rely on binary packaging to do the
right thing on each platform.  On Fedora, the rpmbuild system
passes all the right arguments to the configure script so that
JAGS is installed into /usr/lib64.

 R CMD ldd /usr/local/lib64/R/library/rjags/libs/rjags.so
 will probably confirm that libjags.so.1 is not found.

 If that is not the error, please note what the R posting guide says about
 asking the maintainer.

 --
 Brian D. Ripley,  [EMAIL PROTECTED]
 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, UKFax:  +44 1865 272595

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Re: [R] unable to install rjags on 64-bit Debian Linux (etch)

[plummer]

Hi Roger,

Try this:

install.packages(rjags,configure.args=--with-jags-lib=/usr/local/lib)

The original sin here is that R is installed in the wrong place. By default,
R is installed into /usr/local/lib64 on 64-bit Linux. But this is a
non-standard location on Debian: it should go in /usr/local/lib.
(The Debian binary packages for R put everything in the right place).

I know the rjags configuration needs a bit of work, but a fully functional
version will have to wait until version 2 of the JAGS library.

I hope this helps. If it does not, then write to me off-list.

Martyn

Quoting Roger Levy [EMAIL PROTECTED]:

 While I have been able to install rjags on my Windows computer, oddly I
 have been unable to install rjags successfully on my 64-bit Linux
 compute server (etch, Linux kernel 2.6.18).  I am required to specify
 the JAGS module directory upon installation; when doing this within R, I
 get:


install.packages(rjags,configure.args=--with-jags-modules=/usr/local/lib/JAGS/modules/)

 which works fine, but then trying to load rjags gives an error:

   library(rjags)
 \Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
 '/usr/local/lib64/R/library/rjags/libs/rjags.so':
libjags.so.1: cannot open shared object file: No such file or directory
 Error : .onLoad failed in 'loadNamespace' for 'rjags'
 Error: package/namespace load failed for 'rjags'

 I'm not sure how to read this error.  Does anyone have any suggestions?

 Many thanks,

 Roger



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Re: [R] Building with MKL on Ubuntu

[plummer]

I can see a couple of problems:

1) No -lpthread in --with-blas
2) No -L prefix in the library path in --with-lapack

In addition, I don't think you need to add -lmkl to --with-lapack,
although that is probably harmless.

Martyn

Quoting Prof Brian Ripley [EMAIL PROTECTED]:

 Look in config.log to see what's wrong.  (E.g. is
 /opt/intel/mkl/10.0.2.018/lib/em64t in the ld.so cache?)

 And note the warnings in the manual about using --with-lapack: it is most
 definitely not recommended.

 R-devel would be a better place to ask questions about this.

 On Tue, 4 Nov 2008, Anand Patil wrote:

  Hi all,
  I'm trying to build R from subversion with MKL 10.0.2 on Ubuntu. I tried:
 
  ./configure --with-blas='-L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl
  -lguide' --with-lapack='/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl
  -lmkl_lapack' --enable-R-shlib
 
  and got:
 
  R is now configured for x86_64-unknown-linux-gnu
 
   Source directory:  .
   Installation directory:/usr/local
 
   C compiler:gcc -std=gnu99  -g -O2
   Fortran 77 compiler:   gfortran  -g -O2
 
   C++ compiler:  g++  -g -O2
   Fortran 90/95 compiler:gfortran -g -O2
   Obj-C compiler:
 
   Interfaces supported:  X11
   External libraries:readline
   Additional capabilities:   PNG, JPEG, iconv, MBCS, NLS, cairo
   Options enabled:   shared R library, shared BLAS, R profiling,
  Java
 
   Recommended packages:  yes
 
  but make then builds R's blas, and when I subsequently do linear algebra in
  R it's obviously not multithreading. What am I doing wrong?
 
  Thanks,
  Anand
 
  [[alternative HTML version deleted]]
 
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 --
 Brian D. Ripley,  [EMAIL PROTECTED]
 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, UKFax:  +44 1865 272595

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Re: [R] Installing R in Linux: problems with JAVA packages (rJava, RWeka, ...) ?

[Martyn Plummer]

On Tue, 2008-10-21 at 15:36 +0100, Paulo Cortez wrote:
 Hi,
 
 While in MacOS it is quite simple to install R and Java packages, the 
 same is not true for Linux. I surfed the web and it seems that other 
 users also have similar problems. Perhaps a nice FAQ answer or HOWTO 
 would help...
 
 But here is my situation: I have 2 linux servers, one with Fedora 9 and 
 the other with CentOS5.

Fedora and CentOS do support Java, but not the Sun version since it is
not free software. You would need to buy the commercial Red Hat
Enterprise Linux if you wanted that.

Both Fedora and CentOS provide the java-1.6.0-openjdk and
java-1.6.0-openjdk-devel RPMs.  The post install scripts of these RPMs
will set up your Java environment, including creating the necessary
symbolic links (although you may need to remove your hand-made symbolic
links first to ensure that this works correctly).

There is also GNU java (java-1.5.0-gcj-devel). Although you can install
the GNU and OpenJDK versions in parallel, you can only use one of them
exclusively at any time (the choice is managed using the alternatives
command).  I once ended up with a mixed GNU/OpenJDK Java enviroment
which did not work.  In fact I got exactly the same error message you
did.

continued below ...

 I have installed R (2.7.2 version, with yum) and I tryed to install the 
 RWeka and rJava packages.
 
 After receiving an error, I installed jdk1.6 from java (file:
 jdk-6u10-linux-i586-rpm.bin?AuthParam=1224512972_e5a9932e886a02f44dfdfe48aad02db8TicketId=B%2Fw2nBuFSltLQRRFM1JblgDkGroupName=CDSFilePath=%2FESD5%2FJSCDL%2Fjdk%2F6u10%2Fjdk-6u10-linux-i586-rpm.binFile=jdk-6u10-linux-i586-rpm.bin)
 in both machines.
 
 Then, I had to manually set the java links, using something like:
 
 # rm /usr/bin/java
 # ln -sv /usr/java/default/bin/java /usr/bin/java
 
 (repeat these lines for javac, javadoc, javah, etc..)
 
 Finally I performed (in both machines):
 
 R CMD javareconf (as root)
 
 In Fedora9, I opened R and the package installation went well.
 But in the CentOS5 machine, I received the error:
 -
 checking Java support in R... configure: error: absent
 R was configured without Java support. Please run
 R CMD javareconf
 as root to add Java support to R.
 
 If you don't have root privileges, run
 R CMD javareconf -e
 -
 Since the R CMD javareconf did not work, I tryed instead:
 R CMD javareconf -e
 
 And now I receive the error:
 checking whether JNI programs can be compiled... configure: error: 
 Cannot compile a simple JNI program. See config.log for details.
 
 Currently, I do not know how to resolve this error. Where is the 
 config.log file? As a root, I did: # find / -name config.log .print
 and find no file regarding this JNI error. Also, it is quite difficult 
 for a non expert to resolve this type of errors... Any help?


... You don't see the config.log file because the package is unpacked
and built in a temporary directory.  If you want to inspect the log file
you need to download the package, untar it, and then type R CMD INSTALL
rJava.

In my case, the config.log was not particularly helpful. The linker
complained about not being able to find libjvm, but this was just a
symptom of a broken Java configuration.

I hope this helps.
Martyn

 Regards,

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Re: [R] GPG key not found

[Martyn Plummer]

Have you tried other keys? (mine is 97D3544E if you want to try).
If nothing works then it is probably a firewall problem.  Ask your
network administrator if port 11371 is blocked.

When I had this problem, neither gpg --recv-keys nor the web interface
at wwwkeys.pgp.net worked for me.

Martyn

On Wed, 2008-10-22 at 16:31 +0200, Renaud Gaujoux wrote:
 Hi,
 
 well... that is what I would like to see indeed. :(

 But I keep getting my error, what's bothering me is that the web-based 
 tools also does not find the key...
 Did you also try on http://keyserver.noreply.org/?
 
 thanks
 
 
 Dr Eberhard Lisse wrote:
  gpg: requesting key E2A11821 from hkp server subkeys.pgp.net
  gpg: key E2A11821: public key Vincent Goulet
  [EMAIL PROTECTED] imported
  gpg: no ultimately trusted keys found
  gpg: Total number processed: 1
  gpg:   imported: 1
 
 
  on 10/22/08 3:42 PM Renaud Gaujoux said the following:

  Hi,
  I tried to install R 2.8 on Ubuntu Hardy via the Ubuntu mirroed repository.
  I tried to import the GPG key with:
 
  gpg --keyserver subkeys.pgp.net --recv-key E2A11821
 
  but get the following error:
 
  gpg: requesting key E2A11821 from hkp server subkeys.pgp.net
  gpgkeys: key E2A11821 not found on keyserver
  gpg: no valid OpenPGP data found.
  gpg: Total number processed: 0
 
  I also tried on http://keyserver.noreply.org/ as recommended, but no key
  is found either...
 
  Anybody else gets the error?
 
 
  Thanks
 
  __
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Re: [R] Installing R in Linux: problems with JAVA packages (rJava, RWeka, ...) ?

[Martyn Plummer]

Well this is interesting. I have a working java setup (using OpenJDK).
But I can break it by running R CMD javareconf -e. This command
exports a number of JAVA_* environment variables. The rJava configure
script uses these instead of querying R, but the compilation then fails.

It seems that the crucial difference is that the environment variables
JAVA_CPPFLAGS and JAVA_LIBS contain references to JAVA_HOME that are not
expanded.  With the non-working configuration I get this output from the
configure script:

cpp flags   : '-I$(JAVA_HOME)/../include -I
$(JAVA_HOME)/../include/linux'
java libs   : '-L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64
-L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm'

Whereas with the working R configuration I get the fully expanded
version:

cpp flags   :
'-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux'
java libs   :
'-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib
-ljvm'

Try compiling in a new shell without exporting any of these JAVA_*
variables.

Martyn

On Wed, 2008-10-22 at 12:00 +0100, Paulo Cortez wrote:
 Thanks for the many answers I received.
 
 This is becoming a nightmare and I am concluding that installing java1.6 
 in CentOS5 is particularly hard, specially if you installed previous jdk 
 versions...
 
 I tryed a wide range of solutions. I resume some of them:
 
 1) Tryed to reinstall jdk1.6 and use update-alternatives command;
 1) The CentOS5 howto java guide is outdated and does not work 
 (http://wiki.centos.org/HowTos/JavaOnCentOS);
 2) I installed openjdk, from: http://openjdk.java.net/install/
 I checked if the java was updated with:
 $alternatives --config java
 
 There are 2 programs which provide 'java'.
 
SelectionCommand
 ---
 1   /usr/lib/jvm/jre-1.4.2-gcj/bin/java
 *+ 2   /usr/lib/jvm/jre-1.6.0-openjdk/bin/java
 
 Then, after several R CMD javareconf attemps I got:
 
 --
 Java interpreter : /usr/bin/java
 Java version : 1.6.0_0
 Java home path   : /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre
 Java compiler: /usr/bin/javac
 Java headers gen.: /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../bin/javah
 Java archive tool: /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../bin/jar
 Java library path: 
 $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib
 JNI linker flags : -L$(JAVA_HOME)/lib/i386/server 
 -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L 
 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
 JNI cpp flags: -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
 
 Updating Java configuration in /usr/lib/R
 Done.
 --
 The link files are ok:
 $ ls -la /usr/bin/ja*
 lrwxrwxrwx 1 root root  8 Apr 11  2008 /usr/bin/jade - openjade
 lrwxrwxrwx 1 root root 48 Oct 22 10:52 /usr/bin/java - 
 /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/java
 lrwxrwxrwx 1 root root 49 Oct 22 10:52 /usr/bin/javac - 
 /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javac
 lrwxrwxrwx 1 root root 51 Oct 22 11:19 /usr/bin/javadoc - 
 /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javadoc
 lrwxrwxrwx 1 root root 49 Oct 22 11:18 /usr/bin/javah - 
 /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javah
 lrwxrwxrwx 1 root root 50 Oct 22 10:52 /usr/bin/javaws - 
 /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/bin/javaws
 
 But then I try:
 $ R CMD INSTALL rJava (the rJava.tar.gz was unpacked)
 ...
 checking whether JNI programs can be compiled... configure: error: 
 Cannot compile a simple JNI program. See config.log for details.
 -
 Opening the config.log file I get:
 -
 configure:3880: checking whether JNI programs can be compiled
 configure:3898: gcc -o conftest -O3 -g -std=gnu99 
 -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux   conftest.c 
 -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/l
 ib/i386 -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 
 -L/lib -L/usr/lib -ljvm 5
 /usr/bin/ld: cannot find -ljvm
 collect2: ld returned 1 exit status
 configure:3904: $? = 1
 configure: failed program was:
 |
 | #include jni.h
 | int main(void) {
 | jobject o;
 | JNI_CreateJavaVM(0, 0, 0);
 | return 0;
 | }
 |
 configure:3920: error: Cannot compile a simple JNI program. See 
 config.log for details.
 
 All these attempts took 2 hours of my life, with no results :(((
 
 Regards,

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Re: [R] WG: Problem during porting R-2.7.2 on HP-UP 11.11 PA-Risc

[Martyn Plummer]

On Tue, 2008-09-23 at 15:35 +0200, Peter Dalgaard wrote:
 [EMAIL PROTECTED] wrote:
 
   Claus-Juergen 
   Neumann/BASF-AG/B 
   ASFAn 
  r-help@r-project.org   
   23.09.2008 12:49Kopie 
 
   Thema 
  Problem during porting R-2.7.2 on  
  HP-UP 11.11 PA-Risc
 
 
 
 
 
 
 
 
 
 
 
 
 
  Dear R-Team,
  we had some problem to install R-2.7.2 on HP-UX 11.11 on PA-Risc platform.
 
  1.) i load down the Software and made a extract of the tar-file in a
  specific Directory.
 
  2.) i follow the instructions on the INSTALL file:
   ./configure
 
  3.) during configure we got a error message see below:
   checking for history_truncate_file... no
   configure: error: --with-readline=yes (default) and headers/libs are
  not available
 
  and the configure stops.
 
 
  on the HP-UX server there are the HP Compiler and the GNU compiler with
  gmake and and ... installed.
  Please have a look to my logfiles. Hopefully you had a idea what we can do.
  Thanks a lot for your help

 Attachments are chopped by the mailing list softare, and the r-devel
 list would have been a better choice.
 
 Anyways, the error is what it says: You are trying to use the readline
 library and it or its headers isn't there (at least not where configure
 looks for it). So either install them or use --with-readline=no and live
 without commandline recall. This is explained  at a number of places in
 http://cran.r-project.org/doc/manuals/R-admin.html (search for readline).

Don't forget to also read the platform-specific notes on HP-UX in
appendix C.5 of the same document.  This may help you with any further
problems.


  (See attached file: BASF_CONFIGURE.log.txt)(See attached file:
  config.log.txt)
 
  very best regards
  Claus-Juergen Neumann


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Re: [R] Still no R-2.7.2 rpms for Redhat Enterprise Linux

[Martyn Plummer]

We'll see what we can do.  I have forwarded your email to Bob Kinney,
who builds the RHEL RPMS.

Martyn

On Thu, 2008-09-18 at 14:57 -0700, Waichler, Scott R wrote:
 There's already an announcement about R 2.8.0, and yet there are still
 no R-2.7.2 binaries (rpms) for Redhat Enterprise Linux 4 and 5.  Can the
 usual responsible party get on it?  Can the system be improved to get
 more timely builds out on CRAN?
 
 Thanks,
 Scott Waichler
 Pacific Northwest National Laboratory

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[R] New mailing list R-SIG-Fedora

[Martyn Plummer]

Thanks to Martin Maechler, there is a new special interest group (SIG)
mailing list for users of R on Fedora: http://www.fedoraproject.org

Fedora users will have noticed that RPMs for R 2.7.0 have not yet
arrived through the Fedora Yum channel.  This is because Fedora 9 went
into feature freeze, blocking all updates, before R 2.7.0 was
released.  

However, this is not the only reason for the delay.  The Fedora project
has introduced a peer review system. Package updates must now be tested
before they are pushed through to the yum repository.  The RPMs for R
2.7.0 on Fedora 7, 8, and 9 are currently available on the admin site:

Fedora 9:
https://admin.fedoraproject.org/updates/F9/FEDORA-2008-4012

Fedora 8:
https://admin.fedoraproject.org/updates/F8/FEDORA-2008-4059

Fedora 7:
https://admin.fedoraproject.org/updates/F7/FEDORA-2008-4021

Your help is needed to push these through to the yum repository. If you
are a Fedora user, please download, test and score these RPMs.  You can
do this as an anonymous tester if you wish. Once the karma score
reaches 2, the package will be pushed into stable repository and will
become available through yum.

R packages that are distributed as RPMs must also be peer reviewed.
There is a version of R-Matrix that has been sitting in the testing
queue for Fedora 8 since February...

If you want to do this on a regular basis, please join the R-SIG-Fedora
mailing list, where future announcements on this topic will be posted.
The list is also open to all discussions of interest to Fedora users.

The home page is: https://stat.ethz.ch/mailman/listinfo/r-sig-fedora

Thanks
Martyn


-- 
Martyn Plummer [EMAIL PROTECTED]

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