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

[Dan Tenenbaum]

Hi Nguyen,

> Subject: [R] install "multtest" and "preprocessCore" packages in
> Bioconductor library
> Date: Wed, 30 Nov 2011 09:57:36 -0800
> From: UyenThao Nguyen <unguyen at tethysbio.com>
> To: r-help <r-help at r-project.org>
> CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu>
>
> 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
>

You don't specify what commands you are using to install these packages.

Bioconductor recommends installing packages with biocLite(), like so:

source("http://bioconductor.org/biocLite.R")
biocLite(c("multtest", "preprocessCore"))

Please send the output of those commands, as well as the output of
sessionInfo() so we can help solve your problem.


Thanks
Dan



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