[R] install "multtest" and "preprocessCore" packages in Bioconductor library

[R. Michael Weylandt]

As the posting guide strongly suggests, I think the first step is to
update to R 2.14: there have been changes in package design and I'm
not sure back-compatibility will run that far. Doing so should let you
download fresh binaries straight from BioC.

I'm not sure why you would get compilation errors if you are just
installing a binary -- are you sure you're doing it right? What are
your commands?

I think follow-up should be directed to the dedicated BioConductor
list, but I assume they will tell you the same thing: 1) Update R and
try to install prepackaged libraries; 2) install local copies of the
binaries; 3) only compile from source if needed (you probably don't
have a fortran compiler which seems to be part of the problem)

Michael

On Wed, Nov 30, 2011 at 12:57 PM, UyenThao Nguyen <unguyen at tethysbio.com> wrote:
> Hi All,
>
> I've tried to install these "multtest" and "preprocessCore" packages in Mac, but kept getting error messages. I tried to load the packages using 2 ways:
>
> 1. Installed from BioConductor (sources)
> 2. And installed from BioConductor (binaries)
>
> Both ways, I got these error messages:
>
> For preprocessCore:
> ld: warning: directory '/usr/local/lib' following -L not found
> ld: library not found for -lgfortran
> collect2: ld returned 1 exit status
> make: *** [preprocessCore.so] Error 1
> ERROR: compilation failed for package ‘preprocessCore’
> * removing ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’
> * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’
>
>
>
> For multtest:
> ld: warning: directory '/usr/local/lib' following -L not found
> ** arch - x86_64
>
>
> Looks like the error got to do with L drive, which I don't know how to fix it. Please help. Any suggestions will be greatly appreciated.
>
> Thank you very much,
> Nguyen
>
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