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

[Simon Urbanek]

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?
>

Yes, that sounds like a problem with the BioC builds (libintl.3.dylib  
is really strange - we use libintl.8.dylib as a part of optional Gtk  
on CRAN, but never libintl3.dylib..). I didn't test BioC builds ever  
since we stopped building it on CRAN, but I have heard complains about  
their binaries linking various stuff from /usr/local, so I'd suggest  
to file a bug report with them (BTW: Xcode should not be required from  
binary installs).

Cheers,
S


> Vince Carey reports that a student of his had a similar problem.
>
> Kasper
>
> On Jun 16, 2008, at 6:53 AM, jason smith wrote:
>
>> Thanks Steve,
>>
>> Here is what I get from otool:
>>
>> jason-smiths-macbook:~ sjorges2002$ otool -L /Users/sjorges2002/ 
>> Library/R/2.7/library/affy/libs/i386/affy.so
>> /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so:
>> affy.so (compatibility version 0.0.0, current version 0.0.0)
>> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version  
>> 1.2.3)
>> 	/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/ 
>> libR.dylib (compatibility version 2.7.0, current version 2.7.0)
>> /usr/local/lib/libintl.3.dylib (compatibility version 8.0.0,  
>> current version 8.3.0)
>> /usr/lib/libiconv.2.dylib (compatibility version 5.0.0, current  
>> version 5.0.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current  
>> version 88.3.10)
>> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/ 
>> CoreFoundation (compatibility version 150.0.0, current version  
>> 368.35.0)
>> /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0,  
>> current version 1.0.0)
>>
>> Best
>> Jason
>>
>> --- On Mon, 6/16/08, Steve Lianoglou  
>> <mailinglist.honeypot at gmail.com> wrote:
>>
>>
>>>
>>> You're not doing it right :-)
>>
>>>
>>> otool -L
>>> /Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so
>>>
>>> Let's see what you get from that.
>>>
>>> -steve
>>
>>
>>
>
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