[BioC] Updated BioC 2.2 Mac OS X binary packages soon to be released on bioconductor.org (was Re: [R-SIG-Mac] affy won't load)

[Patrick Aboyoun]

Last night's BioC 2.2 Mac OS X binary packages went well and will soon 
be available on bioconductor.org. These packages make use of the dynamic 
libraries (libgcc_s.1.dylib, libgfortran.2.dylib, libreadline.5.2.dylib, 
and libreadline.dylib) that are distributed with the standard Mac OS X 
build of R 2.7.x. The new packages have been pushed to the web server 
behind bioconductor.org, but due to the file caching by the web server, 
the more popular packages are pulled from the cache rather than the new 
package set. It can sometimes take a few hours for the cache to be 
cleared and for the complete set of Mac OS X binary packages to be 
available.

Here is a look at how the affy and affyio packages are now linking to 
external libraries:

[Examination of affy]
pitt:~/test biocbuild$ otool -L affy/libs/i386/affy.so
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 2.7.1)
    
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
(compatibility version 150.0.0, current version 368.27.0)
    
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgcc_s.1.dylib 
(compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 88.3.3)

[Examination of affyio]
pitt:~/test biocbuild$ otool -L affyio/libs/i386/affyio.so
affyio/libs/i386/affyio.so:
    affyio.so (compatibility version 0.0.0, current version 0.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 88.3.3)
    /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 2.7.1)
    
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
(compatibility version 150.0.0, current version 368.27.0)
    
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgcc_s.1.dylib 
(compatibility version 1.0.0, current version 1.0.0)

If you experience any other related issues along these lines, please 
feel free to e-mail me directly.


Cheers,
Patrick


Patrick Aboyoun wrote:
> Thanks to all for bringing this issue of the BioC 2.2 Max OS X binary 
> packages to light, and I apologize for any inconvenience these 
> non-standard binary packages have caused the BioC user community. If 
> all goes well with the build system tomorrow morning, the Mac OS X 
> binary packages will be produced under the standard Mac OS X R 
> framework. I will send out an e-mail tomorrow morning notifying you on 
> its status.
>
> I don't want to get too much into the gory details of the build 
> system, but I will provide you with a high level synopsis on what 
> caused the breakdown. Back when the Bioconductor core team released 
> BioC 2.2 in May, we had a last minute scramble for the Mac OS X binary 
> packages builds.  Up until release time, we were building the packages 
> on Mac OS X Leopard (10.5.2). It was brought to our attention the week 
> of the release that those builds were not working on Mac OS X Tiger. 
> When we switched to a Tiger build machine, we experienced problems 
> with the png device (type = "quartz", the default, failed to work in 
> our build environment). In order to be expedient we used a custom 
> build of R 2.7.0 to get around this issue. This had the unintended 
> consequence that you discovered. We have since reverted back to using 
> the standard R 2.7.1 build for the Mac and are using a configuration 
> file to set options(bitmapType = "cairo") to get around the png device 
> issue. These new Mac binary package builds will be linking into the 
> dynamic libraries located in the standard R directory 
> /Library/Frameworks/R.framework/Resources/lib.
>
>
> Cheers,
> Patrick

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