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R 2.14.0 on MacBook Pro

8 messages · Federico Calboli, Verbesselt, Jan, Simon Urbanek

Original
Verbesselt, Jan
# 
Dear all,

I have just upgraded from 2.13.2 to 2.14.0 on my mac book pro on 10.6.8 OsX. 
After installing the "zoo" package -  I am unable to load the zoo package in R using R64.app.

What is causing this problem? Everything used to work fine in 2.13.2. Is there anything I need to fix after updating?

Strangely, I noticed that when using Rstudio or R from Terminal -> and loading the zoo package no problem occurs.

Thanks for your help,
Jan


sessionInfo()
install.packages("zoo")
require(zoo)
library(zoo)


.Rprofile: Setting Amsterdam repository
[R.app GUI 1.42 (5933) x86_64-apple-darwin9.8.0]
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
Installing package(s) into ?/Users/janvb/Library/R/2.14/library?
(as ?lib? is unspecified)
trying URL 'http://www.freestatistics.org/cran/bin/macosx/leopard/contrib/2.14/zoo_1.7-6.tgz'
Content type 'application/x-gzip' length 1397025 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb


The downloaded packages are in
	/var/folders/zU/zUFo9cfDGwisjk7fyjDVtk+++TI/-Tmp-//RtmpHiqeQS/downloaded_packages
Loading required package: zoo
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so':
  dlopen(/Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so, 6): Library not loaded: @rpath/R.framework/Versions/2.14/Resources/lib/libR.dylib
  Referenced from: /Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so
  Reason: image not found
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so':
  dlopen(/Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so, 6): Library not loaded: @rpath/R.framework/Versions/2.14/Resources/lib/libR.dylib
  Referenced from: /Users/janvb/Library/R/2.14/library/zoo/libs/x86_64/zoo.so
  Reason: image not found
Error: package/namespace load failed for ?zoo?
Simon Urbanek
# 
Jan,
On Nov 10, 2011, at 6:02 AM, Verbesselt, Jan wrote:

            

      
      
      
    

        
It is probably my fault (details below) - a quick fix is to update your R.app GUI from http://r.research.att.com/

Technical details:

Recent R binaries (but only after 2.14.0 release) use @rpath to allow re-location of the R framework - it means that you can have the entire R in just one icon that you can move around as you please - just like the R.app GUI now except that the entire R is in there and no other dependencies are needed (e.g. you can just put it on a CD or thumb drive). According to Apple documentation the default fallback to @rpath includes /Library/Frameworks which is the location of the R framework when installed, so everything that worked before with absolute paths should be working with @rpath. However, it seems that for some unknown reason the R.app binaries don't fall back to the old @rpath and/or there are some issues combining absolute paths and @rpath. The most recent build of R.app include the LC_RPATH load commands set accordingly so they don't need the fallback. It is indeed startling, because the behavior that you see in Terminal, RStudio etc. is how it is supposed to behave according to Apple documentation. Before I figure out how to solve this you can simply grab more recent R.app.

Thanks,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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I have started a re-build of the packages that were affected so starting tomorrow all you need to do is to update those packages. (This is mainly for people that don't want to touch their R.app - the bottom line is that the issue should go way for anyone installing packages or R later).

Cheers,
Simon

        
On Nov 10, 2011, at 9:41 AM, Simon Urbanek wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Federico Calboli
    

    

      
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On 10 Nov 2011, at 14:41, Simon Urbanek wrote:

        

            

      
      
      
    

        
I did follow the quick fix, and I did upgrade all upgradable packages as for today ( 12 noon-ish GMT, 11/11/11). Still I cannot load the package 'caret'.

I'm on Lion OS 10.7.2 and R 2.14.0 -- R.app GUI 1.42 (5933) x86_64-apple-darwin9.8.0

Cheers

Federico


--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

  
  


  


      

    

    

      
      

        


  

        

      Federico Calboli
    

    

      
      #
    

  


  

      
On 11 Nov 2011, at 12:12, Federico Calboli wrote:

        

            

      
      
      
    

        
I should have added:

            

      
      
      
    

        
Loading required package: lattice
Loading required package: reshape
Loading required package: plyr

Attaching package: ?reshape?

The following object(s) are masked from ?package:plyr?:

    rename, round_any

Loading required package: cluster
Loading required package: foreach
Loading required package: iterators
Loading required package: codetools
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/caret/libs/x86_64/caret.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/caret/libs/x86_64/caret.so, 6): Library not loaded: @rpath/R.framework/Versions/2.14/Resources/lib/libR.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/caret/libs/x86_64/caret.so
  Reason: image not found
Error: package/namespace load failed for ?caret?

bw

F

--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

  
  


  


      

    

    

      
      

        


  

        

      Federico Calboli
    

    

      
      #
    

  


  

      
On 11 Nov 2011, at 12:13, Federico Calboli wrote:

        

            

      
      
      
    

        
My mistake. When I upgraded the R.app GUI I did not change it's name from R to R64, so the R64 GUI did not get upgraded (and the R 32 bit GUI was replaced by the R 64 bit GUI). I have now rectified the issue and all works.

As a aside, it would be helpful if the R.app 64 bit GUI from http://r.research.att.com/ came out of the package with the name R64 given installing R afresh gives two GUIs with two names and it can lead to confusion.

Cheers

F




--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

  
  


  


      

    

    

      
      

        


  

        

      Verbesselt, Jan
    

    

      
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Simon,

I have downloaded the R.app GUI (R-GUI-5944-2.14-leopard-Leopard64.dmg) from http://r.research.att.com/. Everything works fine, when launching the R.app and loading the "zoo" package.
I have deleted the R64.app which was installed with the standard R 2.14.0 currently available at R project website. This R.app is launching the R 64 bit version it seems.

An additional question related to the http://r.research.att.com/ R developers page.  I there a way to set-up some sort of updating mechanism - similar to Linux Ubuntu set-up sources.list - so that R automatically updates (after agreeing) to the most recent stable version?




Report from R.app:
[R.app GUI 1.43 (5944) x86_64-apple-darwin9.8.0]

            

      
      
      
    

        
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

            

      
      
      
    

        
Installing package(s) into ?/Users/janvb/Library/R/2.14/library?
(as ?lib? is unspecified)
trying URL 'http://www.freestatistics.org/cran/bin/macosx/leopard/contrib/2.14/zoo_1.7-6.tgz'
Content type 'application/x-gzip' length 1397206 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb


The downloaded packages are in
	/var/folders/zU/zUFo9cfDGwisjk7fyjDVtk+++TI/-Tmp-//RtmpCVNhCN/downloaded_packages

            

      
      
      
    

        
Loading required package: zoo

Attaching package: ?zoo?

The following object(s) are masked from ?package:base?:

    as.Date, as.Date.numeric

            

      
      
      
    

        
thanks heaps for fast reply and support,
Jan

        
On 10/11/2011, at 3:41 PM, Simon Urbanek wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
Jan,

        
On Nov 12, 2011, at 4:35 AM, Verbesselt, Jan wrote:

        

            

      
      
      
    

        
What you downloaded is the 64-bit version (Leopard64). How you name it is entirely up to you. The CRAN installer names them R.app and R64.app essentially for historical reasons.

            

      
      
      
    

        
The "most recent stable version" is the release version from CRAN (currently 2.14.0). So I don't think you are referring to that. 
If you mean R-patched from R.research.att.com then that binary is built nightly so it doesn't make any sense to have any kind of updating mechanism as it would update all the time. Note that those are different concepts. I was just telling you to update as quick fix, the package binaries have been fixed in the meantime so the release works equally well.

Cheers,
Simon