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

Simon Urbanek simon.urbanek at r-project.org
Thu Jun 19 20:42:10 CEST 2008

On Jun 19, 2008, at 2:03 PM, Kasper Daniel Hansen wrote:

> 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

Definitely, and especially since it doesn't help (see my comments to  
Steve below).

I wouldn't recommend installing gettext (unless you know what you're  
doing) simply because it will modify your system such that all future  
configurations will detect it and behave differently. As long as you  
don't plan to copy anything to another machine it is not a big deal,  
but if you do, you'll learn very quickly why that's a bad idea ;).  
Nonetheless, there are valid cases.

However, as Jan pointed out correctly, this is not the only problem  
that BioC builds have, unfortunately. I can only repeat my plea that I  
sent while ago to the BioC team to fix their Mac builds.

> Kasper
> 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.

Are you? Did you actually test it? I'm pretty sure that you're wrong,  
because the commands below compile libintl.8.dylib(!) and thus won't  
help (that one is fine and part of your Gtk binary). I'm still puzzled  
at where the BioC team gets libintl.3 ...


>> 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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