[BioC] problems to install Bioconductor packages in OSX

[Herve Pages]

Hi Joshua,

Before to go any further, do you have any particular reason to use
R 2.1.0? Last R release is 2.3.0 and all R users are highly encouraged
to use it. On the Bioconductor side, we follow the R development cycle
by releasing a new version of our software a few days after a new R x.y
version has been released (approx. every 6 months) and our release is
aimed to work with this version of R _only_.
Our previous release (BioC 1.7) was aimed to work with R 2.2.0 and our
last release (BioC 1.8, released one month ago) is aimed to work with R 
2.3.0.
If you want to use R 2.1.0 then you will only be able to use BioC 1.6 
which we
don't support anymore.

Best regards,

H.

szhan at uoguelph.ca wrote:
> Dear Bioc users,
> I tried to install some bioconductor packages on our cluster run by OS X 10.4
> with R 2.1.0 and failed as bellow.
> I issued the command as an admistrator and the root user:
>   
>> source("http://www.bioconductor.org/biocLite.R")
>>     
> got Warning message:
> unable to load shared library
> '/common/Frameworks/R.framework/Resources/modules/R_X11.so':
>   dlopen(/common/Frameworks/R.framework/Resources/modules/R_X11.so, 6): Library
> not loaded: /usr/X11R6/lib/libSM.6.dylib
>   Referenced from: /common/Frameworks/R.framework/Resources/modules/R_X11.so
>   Reason: image not foundQuoting dag via RT <inquiry-support at bioteam.net>:
> thus after issuing
>   
>> biocLite()
>>     
> got errors for compilation of several packages for instances:
> make: *** [Biobase.so] Error 1
> ERROR: compilation failed for package 'Biobase'
> make: *** [Biostrings.so] Error 1
> ERROR: compilation failed for package 'Biostrings'
> Loading required package: tools
> collect2: ld returned 1 exit status
> make: *** [affyPLM.so] Error 1
> ERROR: compilation failed for package 'affyPLM'Error in library.dynam(lib,
> package, package.lib) :
>         shared library 'Biobase' not found
> In addition: Warning messages:
> 1: package 'Biobase' contains no R code in: loadNamespace(package,
> c(which.lib.loc, lib.loc))
> 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not found
> Error: package 'Biobase' could not be loaded
> Execution halted
> ERROR: execution of package source for 'annaffy' failed
> . . . etc.
> Would you please help me out?
> Thank you in advance!
> Joshua
>
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>   


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------------------------
Hervé Pagès
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 Phone: (206) 667-5791
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