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")
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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