[R-SIG-Mac] RE: R.matlab

stefano iacus stefano.iacus at unimi.it
Fri Nov 5 14:39:21 CET 2004 

It seems like the problem is in the fact that if R_LIBS is not defined  
the aqua GUI does not define it.
By default, the aqua GUI uses ~user_home/R/library and R.oo is in fact  
installed there (temporarily, then removed on failing).
One temporary solution is the following:
1. authenticate as root from within the Aqua GUI (i.e. click on the  
"lock")
2.  
install.packages("R.classes",contriburl="http://www.maths.lth.se/help/ 
R",lib=.libPaths[2])
this will install the bundle inside the framework.

and I have to figure out how to pass the lib argument to the script.

For some reason, you don't see the output of the package installation  
due to lack of synchronization when you run a script as a root.

FYI: the aqua GUI uses the same install.packages as the console  
version. The problem is that R CMD INSTALL (which is called by that  
function) is not aware of R_LIBS env var which is to the contrary  
needed in this bundle case.

stefano

On Nov 5, 2004, at 1:48 PM, Henrik Bengtsson wrote:

> Thank you. I understand from your reply that there are a few MacOSX  
> versions
> maintained (or similar) and that the one maintained by Stefano Iacus  
> is the
> one giving the problem.
>
> To Stefano Iacus, if you not already know, I suspect that it has to do  
> with
> the order the packages are installed. Under "Packages bundles"
> (http://cran.r-project.org/doc/manuals/R-exts.html#Package%20bundles)  
> it
> says
>
> "The Contains field [in DESCRIPTION] lists the packages, which should  
> be
> contained in separate subdirectories with the names given. During  
> building
> and installation, packages will be installed in the order specified.  
> Be sure
> to order this list so that dependencies are appropriately met."
>
> With the introduction of lazy loading this is important. Before, it  
> did not
> seem to be a requirement in practice. Is this order strictly followed  
> by the
> MacOSX installation scripts?
>
> Just a though.
>
> Henrik
>
>
>> -----Original Message-----
>> From: Anestis Antoniadis [mailto:Anestis.Antoniadis at imag.fr]
>> Sent: Friday, November 05, 2004 1:04 PM
>> To: Henrik Bengtsson
>> Cc: r-sig-mac at stat.math.ethz.ch
>> Subject: Re: [R-SIG-Mac] RE: R.matlab
>>
>>
>> Dear Henrik,
>> dear all,
>> same problem for me on Mac OSX R v 2.0.0.
>> However it works with Jan de Leeuw version.
>> Stefano Iacus is aware of the problem.
>> Best
>> Anestis
>>
>> On Nov 5, 2004, at 11:31 AM, Henrik Bengtsson wrote:
>>
>>> [Sorry if this is a repost, but I got an odd error message
>> previously
>>> trying
>>> to reply to 'r-sig-mac-request at stat.math.ethz.ch']
>>>
>>> Hi. I (the author) got a similar problem report two weeks ago and it
>>> was
>>> also from a person running R v2.0.0 on Mac OS X. I do not
>> have access
>>> to
>>> this system so unfortunately I cannot troubleshoot it myself.
>>>
>>> The solution that worked for this person was to download the bundle
>>> manually
>>>
>>> http://www.maths.lth.se/help/R/R.classes_0.55.tar.gz
>>>
>>> and run
>>>
>>> R CMD INSTALL R.classes_0.55.tar.gz
>>>
>>> from the system's command prompt.
>>>
>>> Does this work?
>>>
>>> If it does, it is a good starting point for troubleshooting. The
>>> problem
>>> seems to be that R.oo is not available (==installed) when
>> it tries to
>>> install R.audio, which depends on R.oo. I'm not 100% sure
>> from your log
>>> (below), if R tried (failed, succeeded?) to install the
>> R.oo package
>>> first,
>>> and then tried to install R.audio (your error message), or if it
>>> starts with
>>> R.audio first.
>>>
>>> Have someone else on the R-SIG-Mac list experienced this? Try
>>>
>>> install.packages("R.classes",
>>> contriburl="http://www.maths.lth.se/help/R")
>>>
>>> Currently, it seems to me that this is a OSX problem only (based on
>>> sample
>>> size n=2). If not, I will check with the r-devel list.
>>>
>>> Best wishes
>>>
>>> Henrik Bengtsson
>>>
>>>
>>>> -----Original Message-----
>>>> From: Nathan Weisz [mailto:Nathan.Weisz at uni-konstanz.de]
>>>> Sent: Thursday, November 04, 2004 5:22 PM
>>>> To: r-sig-mac-request at stat.math.ethz.ch
>>>> Cc: hb at maths.lth.se
>>>> Subject: R.matlab
>>>>
>>>>
>>>> Hi,
>>>>
>>>> one of my favourite packages for R is R.matlab which comes with
>>>> R.classes (from Henrik Bengtsson). After upgrading to R
>> 2.0 on Mac OS
>>>> X I attempted to reinstall this package with:
>>>> install.packages("R.classes",
>>>> contriburl="http://www.maths.lth.se/help/R")
>>>> as described on this webpage:
>>>> http://www.maths.lth.se/help/R/R.classes/
>>>> At the end of the installation I get ugly error messages
>>>> (pasted at end
>>>> of email). Calling R.matlab shows me that it's not installed.
>>>>> library(R.matlab)
>>>> Error in library(R.matlab) : There is no package called 'R.matlab'
>>>>
>>>> Does any one have any hints how to get this working?
>>>>
>>>> Best,
>>>> Nathan
>>>>
>>>>
>>>>
>>>> -----UGLY ERROR MESSAGES-----
>>>> * Installing *source* package 'R.audio' ...
>>>> ** R
>>>> ** data
>>>> ** inst
>>>> ** preparing package for lazy loading
>>>> Loading required package: R.oo
>>>> Error in eval(expr, envir, enclos) : The R.oo package is
>> missing. In
>>>> addition: Warning message: There is no package called 'R.oo' in:
>>>> library(package, character.only = TRUE, logical = TRUE,
>>>> warn.conflicts = warn.conflicts, Execution halted
>>>> ** Removing '/Users/nathan/Library/R/library/R.oo'
>>>> ERROR: lazy loading failed for package 'R.audio'
>>>> ** Restoring previous '/Users/nathan/Library/R/library/R.oo'
>>>> ** Removing '/Users/nathan/Library/R/library/R.audio'
>>>> ** Restoring previous '/Users/nathan/Library/R/library/R.audio'
>>>> ** Removing '/Users/nathan/Library/R/library/R.basic'
>>>> ** Removing '/Users/nathan/Library/R/library/R.colors'
>>>> ** Removing '/Users/nathan/Library/R/library/R.graphics'
>>>> ** Removing '/Users/nathan/Library/R/library/R.io'
>>>> ** Removing '/Users/nathan/Library/R/library/R.lang'
>>>> ** Removing '/Users/nathan/Library/R/library/R.matlab'
>>>> ** Removing '/Users/nathan/Library/R/library/R.ui'
>>>>
>>>> Delete downloaded files (y/N)?
>>>> The packages are in /tmp/Rtmp1305/Rinstdir10d63af1
>>>> Warning messages:
>>>> 1: argument 'lib' is missing: using
>> /Users/nathan/Library/R/library
>>>> in: install.packages("R.classes", contriburl =
>>>> "http://www.maths.lth.se/help/R")
>>>> 2: Installation of package R.classes had non-zero exit status in:
>>>> install.packages("R.classes", contriburl =
>>>> "http://www.maths.lth.se/help/R")
>>>>> install.packages("R.oo",
>>>> contriburl="http://www.maths.lth.se/help/R")
>>>> trying URL `http://www.maths.lth.se/help/R/PACKAGES'
>>>> Content type `application/octet-stream' length 257 bytes opened URL
>>>> ==================================================
>>>> downloaded 257 bytes
>>>>
>>>> Warning messages:
>>>> 1: argument 'lib' is missing: using
>> /Users/nathan/Library/R/library
>>>> in: install.packages("R.oo", contriburl =
>>>> "http://www.maths.lth.se/help/R")
>>>> 2: No package "R.oo" on CRAN. in: download.packages(pkgs, destdir =
>>>> tmpd, available = available,
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>> ====================================================
>> Prof. Anestis ANTONIADIS
>> Laboratoire de Modelisation et Calcul(LMC-IMAG)
>> Universite Joseph Fourier
>> Tour IRMA
>> B.P.53
>> 38041 Grenoble CEDEX 9
>> FRANCE
>>
>> Tel:(33) (0) 476514306
>> Fax:(33) (0) 476631263
>> =======================================================
>>
>>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

More information about the R-SIG-Mac mailing list