[R-SIG-Mac] package installation issues

[David Winsemius]

On Nov 24, 2009, at 3:41 PM, 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?
>
> -Michael
>
>
> *****not from source
>> install.packages("igraph")

The default for install.packages might be for binary installation.  
(What does getOption("pkgType") report? If you took that effort to  
install Xcode, then you must have been thinking of building from  
"source".

?install.packages

-- 
David

> 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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>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT