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

From: Tamas Nepusz
Subject: Re: [igraph] Problem installing igraph R package on 64-bit Mac Pro
Date: Tue, 10 Feb 2009 15:25:40 +0000

Hi Michael,

It seems like the R library depends on the GNU MP Bignum library which is not present in OS X by default (at least I guess so). I guess you can install it from Fink or Darwinports, whichever is more convenient for you. I think it will solve your issues and you will be able to install igraph simply by calling install.packages() from R.


On 2009.02.10., at 15:07, Michael Braun 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 
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?



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

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