[R-SIG-Mac] package installation issues

[Simon Urbanek]

On Nov 24, 2009, at 15:41 , Michael Barnett wrote:

> Hi everyone -
>
> I'm having the same package installation issues with igraph, despite  
> installing Xcode. I don't really know what to do. I'll paste the bug  
> I get below - is there an easy fix for my problem? It seems to be an  
> issue with the fact that R can't find a C compiler I'm guessing  
> since I know that this package uses C code. I installed Xcode, but  
> I'm not terribly informed about how to fix these issues. Any guidance?
>

The error is on my side (Fortran disappeared for some builds on the  
Leopard build machine), you don't really need Xcode at all - please  
just re-install igraph using

install.packages("igraph",,"http://r.urbanek.info")

(CRAN mirrors should pick up the updated binary within a day or two  
but the above will work immediately).

In fact there are several other packages affected, so I'd recommend  
update.packages(checkBuilt=TRUE) to all users (in a day or two or use  
the above master repository).

Thanks,
Simon



>
> *****not from source
>> install.packages("igraph")
> trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/2.10/igraph_0.5.3.tgz'
> Content type 'application/x-gzip' length 3277777 bytes (3.1 Mb)
> opened URL
> ==================================================
> downloaded 3.1 Mb
>
>
> The downloaded packages are in
> 	/var/folders/7J/7JpbFNySGACoH3teAShOLE+++TM/-Tmp-//RtmpFip5QZ/
> downloaded_packages
>> library("igraph")
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library '/Library/Frameworks/R.framework/
> Resources/library/igraph/libs/x86_64/igraph.so':
>   dlopen(/Library/Frameworks/R.framework/Resources/library/igraph/
> libs/x86_64/igraph.so, 10): Symbol not found: ___gmpz_clear
>   Referenced from: /Library/Frameworks/R.framework/Resources/library/
> igraph/libs/x86_64/igraph.so
>   Expected in: dynamic lookup
>
> Error : .onLoad failed in 'loadNamespace' for 'igraph'
> Error: package/namespace load failed for 'igraph'
>
> *****from source
>> install.packages("igraph", type="source")
> trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/igraph_0.5.3.tar.gz'
> Content type 'application/x-gzip' length 1211771 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
> * installing *source* package ‘igraph’ ...
> checking for gcc... no
> checking for cc... no
> checking for cl.exe... no
> configure: error: in `/private/var/folders/7J/7JpbFNySGACoH3teAShOLE++
> +TM/-Tmp-/Rtmptn2nFy/R.INSTALL10d63af1/igraph':
> configure: error: no acceptable C compiler found in $PATH
> See `config.log' for more details.
> ERROR: configuration failed for package ‘igraph’
> * removing ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/
> library/igraph’
> * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.10/
> Resources/library/igraph’
>
> The downloaded packages are in
> 	‘/private/var/folders/7J/7JpbFNySGACoH3teAShOLE+++TM/-Tmp-/ 
> RtmpFip5QZ/
> downloaded_packages’
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("igraph", type = "source") :
>   installation of package 'igraph' had non-zero exit status
> On Nov 12, 2009, at 12:53 PM, Steve Lianoglou wrote:
>
>> Heh ...
>>
>> On Nov 12, 2009, at 12:45 PM, Michael Barnett wrote:
>>
>>> I apologize for not being more precise. I'm pasting the printout I
>>> get below:
>>>
>>> *****
>>>> install.packages("igraph")
>>> trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/2.10/igraph_0.5.2-2.tgz'
>>> Content type 'application/x-gzip' length 3312372 bytes (3.2 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 3.2 Mb
>>>
>>>
>>> The downloaded packages are in
>>> 	/var/folders/7J/7JpbFNySGACoH3teAShOLE+++TM/-Tmp-//RtmpXG1NQC/
>>> downloaded_packages
>>>> library(igraph)
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library '/Library/Frameworks/R.framework/
>>> Resources/library/igraph/libs/x86_64/igraph.so':
>>> dlopen(/Library/Frameworks/R.framework/Resources/library/igraph/
>>> libs/x86_64/igraph.so, 10): Symbol not found: ___gmpz_clear
>>> Referenced from: /Library/Frameworks/R.framework/Resources/library/
>>> igraph/libs/x86_64/igraph.so
>>> Expected in: dynamic lookup
>>>
>>> Error : .onLoad failed in 'loadNamespace' for 'igraph'
>>> Error: package/namespace load failed for 'igraph'
>>> ******
>>
>> ... that's really funny. I just tried to re-install igraph like you
>> did, and now I got the same error :-)
>>
>> Do you have XCode installed? Installing the package from source
>> seems to do the trick:
>>
>> install.packages('igraph', type='source')
>> ... lots of compile info ...
>>
>> Now loading igraph works (I had to restart R ... I guess having
>> tried to load the original compiled package hose the workspace,
>> somehow).
>>
>> I typically install most packages from source, anyway, so I guess
>> this is why I didn't see this before.
>>
>> Does this work for you?
>>
>> -steve
>>
>> btw - I'm on a mac pro w/ snow leopard, not that I'm sure that
>> matters now ...
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> |  Memorial Sloan-Kettering Cancer Center
>> |  Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>
>
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