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

[Dan Tenenbaum]

Hi Nguyen,

On Wed, Nov 30, 2011 at 12:11 PM, UyenThao Nguyen <unguyen at tethysbio.com> wrote:
> Thank you All for your prompt helps.
>
> Dear Dan,
>
> Before I used
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biobase") # GET BIOCONDUCTOR PACKAGE FROM SOURCE
>
> then, I went to "Install packages" in Rgui pointing to BioConductor to load
> these packages in. That was why I got the error messages.
>
> Now, I added
>
> biocLite(c("multtest","preprocessCore")) and saw that the packages were
> saved in
> "/var/folders/9m/9mgg3bdhHcmLfSBpO7I6C++++TI/-Tmp-//Rtmpylgrz5/downloaded_packages",
> which I am not sure where.
>
> #############
>> biocLite(c("multtest","preprocessCore"))
> Using R version 2.10.1, biocinstall version 2.5.11.
> Installing Bioconductor version 2.5 packages:
> [1] "multtest"       "preprocessCore"
> Please wait...
>
> trying URL
> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.10/multtest_2.4.0.tgz'
> Content type 'application/x-gzip' length 1694933 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
>
> trying URL
> 'http://www.bioconductor.org/packages/2.5/bioc/bin/macosx/leopard/contrib/2.10/preprocessCore_1.8.0.tgz'
> Content type 'application/x-gzip' length 235382 bytes (229 Kb)
> opened URL
> ==================================================
> downloaded 229 Kb
>
>
> The downloaded packages are in
> /var/folders/9m/9mgg3bdhHcmLfSBpO7I6C++++TI/-Tmp-//Rtmpylgrz5/downloaded_packages
>
> ########
> Then, I did
>
>> library(multtest)


The fact that this produced no error means that multtest is
successfully installed.

>> ?multtest
> No documentation for 'multtest' in specified packages and libraries:
> you could try '??multtest'
>
>

To get help, do this:
help(package="multtest")


> I don't know how to load these functions after they were saved? I am not a
> computer person, so I don't know what to do when things don't work.

You have already loaded the package; library(packagename) is the way to do it.

This and the help() bit above should get you started.
If you have further questions about these specific packages, please
post to the bioconductor list, after reading our posting guide.

http://bioconductor.org/help/mailing-list/posting-guide/

Thanks,
Dan



>
> Thanks again,
> Nguyen
>
>
>
>
>
>
>
> On Nov 30, 2011, at 10:09 AM, Dan Tenenbaum wrote:
>
> 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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>
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>
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>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>