install "multtest" and "preprocessCore" packages in Bioconductor library

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)

?multtest

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

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