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

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Thu Jun 19 20:03:38 CEST 2008

Another way Jason can get up and run quickly is to do something like

R> options(pkgType = "source")

and then do biocLite. That is probably a better solution than trying  
to install gettext


On Jun 19, 2008, at 10:18 AM, Steve Lianoglou wrote:

> Hi,
> 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
> ./configure
> make
> sudo make install
> HTH,
> -steve
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics, and Systems Biology
> Weill Medical College, Cornell University
> http://cbio.mskcc.org/~lianos

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