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Rpy2 and Mac OS X 10.8.3

15 messages · Craig Watson, cstrato, Roy Mendelssohn - NOAA Federal +2 more

Original
Simon Urbanek
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On Apr 2, 2013, at 9:45 AM, Craig Watson wrote:

            

      
      
      
    

        
Try using valgrind, at a cursory glance this seems like some memory corruption...

However, what makes me really uneasy is that you have a lot of conflicting stuff coming from /opt/local -- in particular it seems as if CRAN R and /opt/local is being mixed up - chances are that you are mixing incompatible binaries. Either build everything (incl. R) the way you do in /opt/local or make sure you don't have duplicated incompatible parts in /ipt/local and the framework. 

Cheers,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
14 days later

    

      
      

        


  

        

      cstrato
    

    

      
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Dear Simon,

On your developer site you mention:
"We use Xcode 4.2 but Xcode 3.2 and higher should work as well. Note 
that you will need Command Line Tools component of Xcode on Mac OS X 
10.7 or higher."

I am running OS X 10.7.5 and XCode 4.2.1 on my Mac, but have not 
downloaded the command line tools. My questions are:

- why do I need the command line tools?

- which version do I need to download from:
https://developer.apple.com/downloads/index.action

There are e.g.
   - Command Line Tools (OS X Lion) for Xcode - October 2012
     (it is not mentioned which version of Xcode)
   - Command Line Tools (OS X Lion) for Xcode - November 2012
     (Xcode 4.3 is mentioned but it is nor clear if it works with 4.2.1)
   - Command Line Tools (OS X Lion) for Xcode - April 2013
     (Xcode 4.6.2 is mentioned but it is nor clear if it works with 4.2.1)

   (BTW, the Preferences for Xcode 4.2.1 do not list Command Line Tools 
in the Install window.)

- do the Command Line Tools update clang/clang++?

The reason for my question is that in order to compile the C++ code in 
my package with clang I need at least version 3.1 since 3.0 results in 
an error.

Best regards,
Christian

  
  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Sorry, it seems that I have used another thread by mistake, Christian

        
On 4/16/13 9:13 PM, cstrato wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Roy Mendelssohn - NOAA Federal
    

    

      
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Hi:

The command line tools can be installed once you have Xcode by stating Xcode, going to "Preference" in the File menu and then there is a "Download" option.  That is where you can install the CLI.

You may have to give a terminal command the first time to point to it once installed - I would shave to look that up - I know this had to be done for Fink.

HTH,

-Roy M.

        
On Apr 16, 2013, at 12:13 PM, cstrato <cstrato at aon.at> wrote:

        

            

      
      
      
    

        

      
      
    

        
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

  
  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Thank you, but as I have mentioned already: "the Preferences for Xcode 
4.2.1 do not list Command Line Tools in the Install window."

Best regards,
Christian

        
On 4/16/13 9:20 PM, Roy Mendelssohn - NOAA Federal wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Apr 16, 2013, at 3:13 PM, cstrato wrote:

        

            

      
      
      
    

        
Because Xcode no longer installs compilers, linkers etc. in the system, so you won't be able to run them.

            

      
      
      
    

        
It doesn't really matter (it may matter in the future, because Apple has announced that they'll be removing llvm-gcc from Xcode) - latest should be fine for now. The version is independent of your Xcode -- in fact if you download it by hand, you don't even need Xcode at all.

            

      
      
      
    

        
I'm not sure what you mean by "Install window", but as Roy said, you'll find it in the download section of the preferences.

            

      
      
      
    

        
Yes

            

      
      
      
    

        
You'll need to tweak your local ~/.R/Makevars for that to work since CRAN's R uses llvm-gcc.

Cheers,
Simon

  
  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Dear Simon,

Thank you for your explanation, and see below.

Best regards,
Christian

        
On 4/16/13 9:30 PM, Simon Urbanek wrote:

            

      
      
      
    

        
It seems that my version of Xcode 4.2.1 does have all compilers 
installed, including clang, but version 3.0:
$ clang -v
Apple clang version 3.0 (tags/Apple/clang-211.12) (based on LLVM 3.0svn)
Target: x86_64-apple-darwin11.4.2

            

      
      
      
    

        
When I open the Preferences and go to the download section I see a 
checkbox "Check for and install updates automatically", and below the 
list of items, which are:
- iOS 4.3 Simulator (499.2 MB)
- iOS 4.0 - 4.1 Device Debugging Support (505.1 MB)
- iOS 3.0 - 3.2.2 Device Debugging Support (686.3 MB)
None of these three items do I want to install since the download would 
be 1.7 GB and my internet connection is not very fast.

            

      
      
      
    

        
This is good news.

            

      
      
      
    

        
This seems not to be possible since then I cannot compile my C++ code at 
all. It seems to interfere with the ROOT framework compiled with clang 
and does not find an include file. My Makefile depends on the ROOT 
config file.

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Roy Mendelssohn - NOAA Federal
    

    

      
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My apologies, I didn't notice carefully that you were using Xcode 4.2.1.  But Google is your friend,  Apple has changed the name of what you need to download, see:

http://comments.gmane.org/gmane.os.apple.macports.user/26340

HTH.

-Roy

        
On Apr 16, 2013, at 12:44 PM, cstrato <cstrato at aon.at> wrote:

        

            

      
      
      
    

        

      
      
    

        
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

  
  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Dear Roy,

Thank you for this info. It seems that only the versions of Xcode which 
you download from the AppStore need the Command Line Tools installed.
Nevertheless, in order to install a new version of clang I need to 
install the CLTs.

Best regards,
Christian

        
On 4/16/13 9:51 PM, Roy Mendelssohn - NOAA Federal wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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On 16/04/2013 21:03, cstrato wrote:

            

      
      
      
    

        
In our experience all versions since 4.5 do, wherever you install them 
from.   People who use long-outdated versions of tools cannot expect the 
current instructions to apply to them. And the R manual does make that 
clear:

?Command Line Tools for Xcode? used to be part of the Apple Developer 
Tools (?Xcode?) but nowadays need to be installed separately. They can 
be downloaded from http://developer.apple.com/devcenter/mac/ (you will 
need to register there) or if you have a recent Xcode installed (from 
the App Store or from https://developer.apple.com/devcenter/mac/) you 
can install the command-line tools from within Xcode, from the 
?Downloads? pane in the ?Preferences?.

Note 'used', 'nowadays', 'recent'.

            

      
      
      
    

        
And isn't it nice of Apple to allow you to download them separately?

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Apr 16, 2013, at 4:03 PM, cstrato wrote:

        

            

      
      
      
    

        
No, it's rather your Xcode is so old that it had CLI embedded, new ones don't.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Dear Prof. Ripley, dear Simon,

Thank you for this information about Xcode and CLTs.

Since I have heard that R and Bioconductor packages should in the future 
be built with clang since Apple will be discontinuing support of gcc, my 
question is:

- Which version of Xcode and/or CLTs should Snow Leopard users install 
in the future? (the last official version for Snow Leopard is xcode_3.2.6)

- Which version of Xcode and/or CLTs should Lion/Mountain Lion users 
install so that they can still compile their packages with gcc, too?
(the current version is xcode_4.6.2)

 From the discussion I understand that it is no longer necessary to 
install Xcode at all, installing CLTs is sufficient. Is this  correct?

Best regards,
Christian

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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> be built with clang since Apple will be discontinuing support of gcc, my
 > question is:

I've not heard that, and you give no reference.  It's a pretty safe 
prediction except for timing: it could be a year away.  So your 
questions are not relevant until it is announced.  The documentation in 
the current R manuals is currently the correct advice.

Apple have announced the imminent discontinuation of llvm-gcc, and we 
take that to mean it will not be in Xcode 4.7 (or 5.0 if that is 
released first).  That would mean that once that is released, for most 
users of Lion and later llvm-gcc will disappear (as most users will get 
an automatic upgrade from the AppStore, or as in my case, the sysadmins 
will push out an update).

So we have been working hard on making R and CRAN packages installable 
using clang (there were too many problems at decision time for 3.0.0). 
How to switch a CRAN binary installation to use clang[++] is in the R >= 
3.0.0 manuals.  That may not work for packages with configure scripts: 
for that you may need R-patched.

There are now only seven CRAN packages which have bugs which stop 
installation under clang, and all the maintainers have been sent 
patches.  (Two of those do not install under gcc 4.8.0 either.)

Very likely at some point Simon will switch the CRAN binary distribution 
to use clang, but the real point is that many end-users will need to do 
so soon.

Given that R 3.0.0 supports OS 10.6 (Snow Leopard), it is likely that we 
will do so for all of the 3.0.x series, even though 10.6 will almost 
certainly reach end-of-life well before 3.1.0 is due.  In that case the 
CRAN builder could stick with llvm-gcc for that series, but it may prove 
more convenient for end-users to switch to the distribution to clang 
before then.  Only time will tell.

        
On 17/04/2013 18:45, cstrato wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      cstrato
    

    

      
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Dear Prof. Ripley,

Thank you for this extensive information.

You mention that you have been working hard on making R and CRAN 
packages installable using clang, which is quite an effort.

Currently, the Bioconductor maintainers are doing the same, i.e. 
checking which BioC packages are installable using clang, and I was 
informed that my package 'xps' cannot be installed using clang.

In my case the main problem seems to be that the version of clang used 
has a bug which prevents compilation of xps (and the necessary ROOT C++ 
framework).

Concretely, both the Bioconductor server running Snow Leopard and my 
Snow Leopard Mac have versions of Xcode, which include clang Version 
3.0. In order to compile ROOT successfully, at least clang Version 3.1 
is necessary, see:
http://root.cern.ch/phpBB3/viewtopic.php?f=3&t=14614#p62969

On my Mac running Lion (10.7.5) I have currently also installed Xcode 
4.2.1 which contains clang Version 3.0, so I could reproduce this error 
also on Lion. After downloading the the 'Command Line Tools (OS X Lion) 
for Xcode - March 2013' from the Apple developer site the version of 
clang is now:
$ clang -v
Apple LLVM version 4.2 (clang-425.0.27) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin11.4.2

Using this version I could successfully compile both ROOT and xps. The 
problem is that I do not know how to obtain a more recent version of 
clang for Snow Leopard, the system currently running on the BioC server.

I would very much appreciate if you could propose a solution for this 
problem.

Thank you in advance.
Best regards,
Christian

        
On 4/18/13 11:03 AM, Prof Brian Ripley wrote: