[Rd] Problem with rgl into MAC OS X

2007-10-05 Thread Gustavo H. Esteves 
Dear R Developers,

I'm developing an R package that I had submitted to Bioconductor project.
This package uses the rgl package to do some tri-dimensional scatter pĺots.
I only work with linux (ubuntu 7.04) system and Windows XP. In both of them
the rgl package works fine. But now, bioconductor team is checking my
package with Mac OS X (version 10.4.10) and the function is giving the
following error in this platform:

Error in rgl.open() :
  X11 protocol error: BadMatch (invalid parameter attributes)
Calls: plot -> plot.maigesClass ->  -> rgl.open -> .C
Execution halted

I'm sorry, but I can' t  provide more information about the problem, as I
don't have access to a MAC PC.
Could you help me to solve this problem? Thank you in advance!

Gustavo Esteves




-- 
*

 "The truth you speak has no past and no
   future. It is, and that's all it needs to be."

 "A verdade que você fala não tem passado
  nem futuro. Ela é,  e isso é tudo que ela
  precisa ser."

 Richard Bach

*


   Gustavo Henrique Esteves

   Departamento de Matemática e Estatística,
   Centro de Ciências e Tecnologia,
   Universidade Estadual da Paraíba.

   e-mail: [EMAIL PROTECTED]

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Re: [Rd] Building package with R 2.6.0 on Windows/Cygwin gives error with tar

2007-10-05 Thread Prof Brian Ripley 
Try setting TAR to 'tar --force-local'.

This should be the default under Windows, but a typo was introduced in R 
2.6.0 after it was tested.

On Thu, 4 Oct 2007, Kevin Wright wrote:

> My setup:
> Windows XP, R-2.6.0, Cygwin (not the Rtools version)
>
> When I tried to build a package, I was given this message:
> tar: c\:/X/Rpkgs/Drydown_1.41.tar: Cannot open: Input/Output error
>
> Even manually typing the following caused the same error:
> tar chf 'c:/X/Rpkgs/Drydown_1.41.tar' Drydown
>
> I looked at the 2.5.1 and 2.6.0 build scripts.  After restoring this
> section to the 2.6.0 build script:
>  ## workaround for paths in Cygwin tar
>  $filepath =~ s+^([A-Za-z]):+/cygdrive/\1+;
>  }
> then $filepath evaluates to
>  /cygdrive/c/X/Rpkgs/Drydown_1.41.tar
> and I was able to build packages again.
>
> (Posted in case someone else has the same problem and/or finds this useful.)

It WOULD have been useful if you had tested in the alpha/beta/RC period 
and not immediately after release.  (I believe this has been asked of you 
before.)

-- 
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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[Rd] R-2.6.0 package check problems

2007-10-05 Thread Robin Hankin 
Hello


One of my packages, untb_1.3-2, passes R CMD check under
MacOSX (and apparently the systems used in the package check
summary page on CRAN) but fails with the following message on
R-2.6.0.tgz compiled last night on my (home) linux box.  I hasten
to add that I have never seen this error before on home-compiled
pre-releases of R-2.6.0.

Can anyone help me understand what is going on?


localhost:~/scratch%R CMD check untb_1.3-2.tgz

[snip]

creating untb-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'untb-Ex.R' failed.
The error most likely occurred in:

 > ### * butterflies
 >
 > flush(stderr()); flush(stdout())
 >
 > ### Name: butterflies
 > ### Title: abundance data for butterflies
 > ### Aliases: butterflies butterfly
 > ### Keywords: datasets
 >
 > ### ** Examples
 >
 > data(butterflies)
 > plot(butterflies, uncertainty=TRUE)
Error in log(theta) :
   could not find symbol "base" in environment of the generic function
Calls: plot ... optimal.theta -> optimize ->  -> f -> log
Execution halted







localhost:~/scratch%R
 > sessionInfo()
R version 2.6.0 (2007-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=e 
n_US;LC_
MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M 
EASUREME
NT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15
 > R.version
_
platform   i686-pc-linux-gnu
arch   i686
os linux-gnu
system i686, linux-gnu
status
major  2
minor  6.0
year   2007
month  10
day03
svn rev43063
language   R
version.string R version 2.6.0 (2007-10-03)
 >
 >







--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743

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Re: [Rd] R-2.6.0 package check problems

2007-10-05 Thread Uwe Ligges 


Robin Hankin wrote:
> Hello
> 
> 
> One of my packages, untb_1.3-2, passes R CMD check under
> MacOSX (and apparently the systems used in the package check
> summary page on CRAN) but fails with the following message on
> R-2.6.0.tgz compiled last night on my (home) linux box.  I hasten
> to add that I have never seen this error before on home-compiled
> pre-releases of R-2.6.0.
> 
> Can anyone help me understand what is going on?


- I only see version 1.3-0 of your package passing the checks on CRAN.
- Do you have set R_LIBS inappropriate for your new R version or are you 
using some other binary packages compiled with a former version of R?

Uwe





> 
> localhost:~/scratch%R CMD check untb_1.3-2.tgz
> 
> [snip]
> 
> creating untb-Ex.R ... OK
> * checking examples ... ERROR
> Running examples in 'untb-Ex.R' failed.
> The error most likely occurred in:
> 
>  > ### * butterflies
>  >
>  > flush(stderr()); flush(stdout())
>  >
>  > ### Name: butterflies
>  > ### Title: abundance data for butterflies
>  > ### Aliases: butterflies butterfly
>  > ### Keywords: datasets
>  >
>  > ### ** Examples
>  >
>  > data(butterflies)
>  > plot(butterflies, uncertainty=TRUE)
> Error in log(theta) :
>could not find symbol "base" in environment of the generic function
> Calls: plot ... optimal.theta -> optimize ->  -> f -> log
> Execution halted
> 
> 
> 
> 
> 
> 
> 
> localhost:~/scratch%R
>  > sessionInfo()
> R version 2.6.0 (2007-10-03)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=e 
> n_US;LC_
> MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M 
> EASUREME
> NT=en_US;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15
>  > R.version
> _
> platform   i686-pc-linux-gnu
> arch   i686
> os linux-gnu
> system i686, linux-gnu
> status
> major  2
> minor  6.0
> year   2007
> month  10
> day03
> svn rev43063
> language   R
> version.string R version 2.6.0 (2007-10-03)
>  >
>  >
> 
> 
> 
> 
> 
> 
> 
> --
> Robin Hankin
> Uncertainty Analyst
> National Oceanography Centre, Southampton
> European Way, Southampton SO14 3ZH, UK
>   tel  023-8059-7743
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] R-2.6.0 package check problems

2007-10-05 Thread Thomas Petzoldt 
Robin Hankin wrote:
 > Hello
 >
 >
 > One of my packages, untb_1.3-2, passes R CMD check under
 > MacOSX (and apparently the systems used in the package check
 > summary page on CRAN) but fails with the following message on
 > R-2.6.0.tgz compiled last night on my (home) linux box.  I hasten
 > to add that I have never seen this error before on home-compiled
 > pre-releases of R-2.6.0.
 >
 > Can anyone help me understand what is going on?

Hi Robin,

congratulations to your published article about untb ;-)

One possible explanation is that your examples use random numbers which 
may be different ones during the CRAN check. I had this problem with 
another package where a "rare random number event" lead to 
non-convergence of optim during the package check. You may use 
set.seed() as a first aid and then try to stabilize your algorithms.

BTW: untb_1.3-2.tar.gz passed the check just now on my system: R 2.7.0 
Under development (unstable), svn rev 43092 (5. Oct), i386-pc-mingw32


Thomas P.


-- 
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie[EMAIL PROTECTED]
01062 Dresden  http://tu-dresden.de/hydrobiologie/
GERMANY

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Re: [Rd] Building package with R 2.6.0 on Windows/Cygwin gives error with tar

2007-10-05 Thread Kevin Wright 
I tried setenv TAR="tar --force-local" and also tried changing the
build script directly to
R_system(join(" ",
  ("tar --force-local -chf",
   &shell_quote_file_path($filepath),
   "$pkgname")));
but still had this error:
tar: Cannot execute remote shell: No such file or directory
tar: c\:/x/rpkgs/Drydown_1.41.tar: Cannot open: Input/Output error

Replacing R_system with print confirms that $filepath does not have
the backslash.

Curiously, at the bash prompt, this does work:
tar --force-local -chf "c:/X/Rpkgs/Drydown_1.41.tar" Drydown

Maybe a confusion between R_system and bash ???

I'm happy to help test this further, but with the hack reported at the
start of this thread I'm also content to let this drop (or go off
list).

Kevin Wright



On 10/5/07, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> Try setting TAR to 'tar --force-local'.
>
> This should be the default under Windows, but a typo was introduced in R
> 2.6.0 after it was tested.
>
> On Thu, 4 Oct 2007, Kevin Wright wrote:
>
> > My setup:
> > Windows XP, R-2.6.0, Cygwin (not the Rtools version)
> >
> > When I tried to build a package, I was given this message:
> > tar: c\:/X/Rpkgs/Drydown_1.41.tar: Cannot open: Input/Output error
> >
> > Even manually typing the following caused the same error:
> > tar chf 'c:/X/Rpkgs/Drydown_1.41.tar' Drydown
> >
> > I looked at the 2.5.1 and 2.6.0 build scripts.  After restoring this
> > section to the 2.6.0 build script:
> >  ## workaround for paths in Cygwin tar
> >  $filepath =~ s+^([A-Za-z]):+/cygdrive/\1+;
> >  }
> > then $filepath evaluates to
> >  /cygdrive/c/X/Rpkgs/Drydown_1.41.tar
> > and I was able to build packages again.
> >
> > (Posted in case someone else has the same problem and/or finds this useful.)
>
> It WOULD have been useful if you had tested in the alpha/beta/RC period
> and not immediately after release.  (I believe this has been asked of you
> before.)
>
> --
> 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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[Rd] problem with building package in R 2.6.0

2007-10-05 Thread G.J.A.Fox 
Hello,

 

I can nolonger build R packages in R 2.6.0 (win xp). I get the error
message 'sh' is not recognized as an internal

 or external command. In earlier versions of R I had no problems. Maybe
that someone can help me with this.

 

Jean-Paul Fox.  

 

 

C:\PROGRA~1\R\R-2.6.0\bin>Rcmd build --force --binary C:\Temp\R260\mlirt

* checking for file 'C:\Temp\R260\mlirt/DESCRIPTION' ... OK

* preparing 'C:\Temp\R260\mlirt':

* checking DESCRIPTION meta-information ...'sh' is not recognized as an
internal

 or external command,

operable program or batch file.

'sh' is not recognized as an internal or external command,

operable program or batch file.

 OK

* removing junk files

'sh' is not recognized as an internal or external command,

operable program or batch file.

'sh' is not recognized as an internal or external command,

operable program or batch file.

'sh' is not recognized as an internal or external command,

operable program or batch file.

Error: cannot open file 'mlirt/DESCRIPTION' for reading

 

 

 

__



dr.ir. G.J.A. Fox

Twente University
Faculty of Behavioural Sciences

Department of Research Methodology, Measurement and Data Analysis 

PO. Box 217, 7500 AE Enschede
The Netherlands



E-Mail [EMAIL PROTECTED]

HomePage http://users.edte.utwente.nl/Fox

Voice +31 (0)53 4893326
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Re: [Rd] problem with building package in R 2.6.0

2007-10-05 Thread Prof Brian Ripley 
On Fri, 5 Oct 2007, [EMAIL PROTECTED] wrote:

> Hello,
>
>
>
> I can nolonger build R packages in R 2.6.0 (win xp). I get the error
> message 'sh' is not recognized as an internal
>
> or external command. In earlier versions of R I had no problems. Maybe
> that someone can help me with this.

You can: read the R-admin manual and make sure you have the correct tools 
installed _and in your path_.



>
>
>
> Jean-Paul Fox.
>
>
>
>
>
> C:\PROGRA~1\R\R-2.6.0\bin>Rcmd build --force --binary C:\Temp\R260\mlirt
>
> * checking for file 'C:\Temp\R260\mlirt/DESCRIPTION' ... OK
>
> * preparing 'C:\Temp\R260\mlirt':
>
> * checking DESCRIPTION meta-information ...'sh' is not recognized as an
> internal
>
> or external command,
>
> operable program or batch file.
>
> 'sh' is not recognized as an internal or external command,
>
> operable program or batch file.
>
> OK
>
> * removing junk files
>
> 'sh' is not recognized as an internal or external command,
>
> operable program or batch file.
>
> 'sh' is not recognized as an internal or external command,
>
> operable program or batch file.
>
> 'sh' is not recognized as an internal or external command,
>
> operable program or batch file.
>
> Error: cannot open file 'mlirt/DESCRIPTION' for reading
>
>
>
>
>
>
>
> __
>
>
>
> dr.ir. G.J.A. Fox
>
> Twente University
> Faculty of Behavioural Sciences
>
> Department of Research Methodology, Measurement and Data Analysis
>
> PO. Box 217, 7500 AE Enschede
> The Netherlands
>
>
>
> E-Mail [EMAIL PROTECTED]
>
> HomePage http://users.edte.utwente.nl/Fox
>
> Voice +31 (0)53 4893326
> __
>
>
>
>
>   [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
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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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[Rd] 'R CMD build' and file permissions

2007-10-05 Thread Herve Pages 
Hi,

When building a source package on Linux with 'R CMD build',
the files in the resulting tarball don't have the original
permissions.
The problem is that the packages I want to build include an SQLite
data base (an .sqlite file) and, before I run 'R CMD build', I've
made this file read-only (chmod 444) because I want this DB to be
read-only. Then if I install by running 'R CMD INSTALL' directly on
the source directory, everything works as expected (the permissions
of the installed .sqlite file are conserved). But if I run 'R CMD build'
in order to produce the tarballs (I need to distribute those packages),
then, when the user will install them, the SQLite DBs will not be
read-only anymore.

Is there a way to prevent 'R CMD build' from changing the permissions
of the source files?
Thanks in advance!

Cheers,
H

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