Dan Tenenbaum
2011-Nov-30 18:09 UTC
[R] install "multtest" and "preprocessCore" packages in Bioconductor library
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> ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
UyenThao Nguyen
2011-Nov-30 20:11 UTC
[R] 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@tethysbio.com<mailto:unguyen@tethysbio.com>>
To: r-help <r-help@r-project.org<mailto:r-help@r-project.org>>
CC: uth.nguyen@ucdavis.edu<mailto:uth.nguyen@ucdavis.edu>
<uth.nguyen@ucdavis.edu<mailto:uth.nguyen@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
______________________________________________
R-help@r-project.org<mailto:R-help@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org<mailto:R-help@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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