[R-SIG-Mac] [BioC] affy won't load

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Jun 19 19:18:47 CEST 2008


On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote:

> Ok, I will take this over to the R-SIG-Mac list and cc Herve who is  
> the build manager of Bioconductor. I suspect that something is wrong  
> with the Bioconductor builds.
> Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook  
> running 10.5.3. He says he has Xcode 3.0 installed. He tries to  
> install the binary version of aff from Bioconductor using the normal
>  biocLite("affy")
> However, even though the tarball downloads and gets installed, the  
> package won't load. It complains that it needs the library /usr/ 
> local/lib/libintl.3.dylib (and an otool -L really confirms this),  
> but apparently this files does not exists. I am a bit surprised that  
> the binary version links to something in /usr/local. I have this  
> file on my PPC G4 running 10.5.3. As I see it, this should work out  
> of the box with the system Jason is running. Does anyone have any  
> good ideas? My hunch is that something might be up with the binary  
> builds?

Just so Jason can get up and running quickly (and not have to wait for  
this to get sorted out in the builds or whatever), I would recommend  
as a band-aid procedure to just install gettext for now, as I am  
fairly certain that this will provide the /usr/local/lib/libintl. 
3.dylib that he is missing.

I gather that he might not be very comfortable from the command line,  
so following these steps in a terminal session should do the trick:

cd /tmp
curl http://mirrors.usc.edu/pub/gnu/gettext/gettext-0.17.tar.gz | tar xz
cd gettext-0.17
sudo make install


Steve Lianoglou
Graduate Student: Physiology, Biophysics, and Systems Biology
Weill Medical College, Cornell University


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