Re: [igraph] Problem installing igraph R package on 64-bit Mac Pro

[Gábor Csárdi]

This is not easy to solve, because I don't have a mac and Apple does
not let us run OSX in a virtual machine....

On Tue, Feb 10, 2009 at 4:33 PM, Michael Braun <address@hidden> wrote:
> I was using
>
>  install.packages("igraph",type="source")
>
> from wtihin R.  I just tried R CMD INSTALL igraph from the bash shell, and
> got the same result.

Could you send the whole output? I suspect that ./configure is not
even run on your system, I don't know why....

> I also installed the gmp library, and got the same problem.

For the GMP version to work, you need to install the binary version of
the package. You tried that? Check the igraph.so file in the package,
perhaps you have 'ldd' on OSX, that tells to which dynamic libraries
igraph links to and whether your linker is able to find them.

G.

ps. Please stay on the list, just to make the archive more useful.
Thanks. Btw. if you don't sign up, you might miss some answers,
because they are normally sent only to the list.

> On Feb 10, 2009, at 10:28 AM, Gábor Csárdi wrote:
>
>> Michael, the error message for the binary package means that it was
>> compiled with the GMP library. (See http://gmp.darwinports.com/)
>> Perhaps if you install that, then it will be fine.
>>
>> The R package is usually compiled without this library, so I don't
>> know why this wasn't the case for the one you downloaded.
>>
>> The compilation failure is also strange a bit, it looks like R is
>> ignoring some configuration files in the package. Just to be sure, you
>> did the compilation with
>>
>> R CMD INSTALL igraph_0.5.1.tar.gz
>>
>> right?
>>
>> G.
>>
>> On Tue, Feb 10, 2009 at 4:07 PM, Michael Braun <address@hidden> wrote:
>>>
>>> Hi.  First, thank you for creating and maintaining the igraph R package.
>>>  I
>>> use it quite often and find it to be very usefull.
>>>
>>> However, I am having trouble installing a 64-bit version in R.  If I
>>> install
>>> the binary, downloaded from CRAN, and then load it, I get:
>>>
>>>> install.packages("igraph",repos="http://stat.cmu.edu/R/CRAN";)
>>>
>>> trying URL
>>>
>>> 'http://stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/2.8/igraph_0.5.1.tgz'
>>> Content type 'application/x-gzip' length 3058038 bytes (2.9 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 2.9 Mb
>>>
>>>
>>> The downloaded packages are in
>>>
>>>
>>> /var/folders/6g/6gqJUHG-FsGAUUywFq+B3U++q3w/-Tmp-//RtmpmuFm5c/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'
>>>>
>>>
>>>
>>>
>>>
>>> If I try to compile from source, I eventually get:
>>>
>>> gcc-4.2 -arch x86_64 -std=gnu99
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> -I/Library/Frameworks/R.framework/Resources/include/x86_64
>>> -I/usr/local/include -I/usr/local/include/apophenia -I/usr/local/include
>>> -Wall -O3 -g -p -pg -DHAVE_INLINE  -fPIC  -Wall -O3 -g -p -pg
>>> -DHAVE_INLINE
>>> -c foreign.c -o foreign.o
>>> foreign.c: In function 'igraph_write_graph_gml':
>>> foreign.c:2367: error: 'PACKAGE_VERSION' undeclared (first use in this
>>> function)
>>> foreign.c:2367: error: (Each undeclared identifier is reported only once
>>> foreign.c:2367: error: for each function it appears in.)
>>> foreign.c: In function 'igraph_write_graph_dot':
>>> foreign.c:2603: error: 'PACKAGE_VERSION' undeclared (first use in this
>>> function)
>>> make: *** [foreign.o] Error 1
>>> chmod:
>>> /Library/Frameworks/R.framework/Resources/library/igraph/libs/x86_64/*:
>>> No
>>> such file or directory
>>> ERROR: compilation failed for package 'igraph'
>>> ** Removing '/Library/Frameworks/R.framework/Resources/library/igraph'
>>> ** Restoring previous
>>> '/Library/Frameworks/R.framework/Resources/library/igraph'
>>>
>>> I have no problems with a 32-bit R build.
>>>
>>> By the way, I have an Intel-based Mac Pro, running Leopard (10.5.6).  The
>>> R
>>> version is 2.8.0.
>>>
>>> Ideally, I'd just want to install the binary, but neither approach seems
>>> to
>>> work.
>>>
>>> Can you help?
>>>
>>> Thanks,
>>>
>>> Michael
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------
>>> Michael Braun
>>> Homer A. Burnell Career Development Professor, and
>>>      Assistant Professor of Management Science (Marketing Group)
>>> MIT Sloan School of Management
>>> One Amherst St., E40-169
>>> Cambridge, MA 02142
>>> address@hidden
>>> 617-253-3436
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden>     UNIL DGM
>
> -------------------------------------------
> Michael Braun
> Homer A. Burnell Career Development Professor, and
>        Assistant Professor of Management Science (Marketing Group)
> MIT Sloan School of Management
> One Amherst St., E40-169
> Cambridge, MA 02142
> address@hidden
> 617-253-3436
>
>
>
>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM