[BioC] installing 'lme4' package fails

James W. MacDonald jmacdon at med.umich.edu
Tue Jul 6 15:37:41 CEST 2010


Hi Tim,

On 7/6/2010 7:59 AM, Tim Smith wrote:
> Hi,
>
> I was trying to install the lme4 package, but the installation fails. Here are my commands and output, alongwith the sessionInfo:
>
>> source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>> biocLite("lme4")
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "lme4"
> Please wait...

Although biocLite() will install lme4:

 > biocLite("lme4")
Using R version 2.11.0, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] "lme4"
Please wait...

trying URL 
'http://cran.fhcrc.org/bin/windows/contrib/2.11/lme4_0.999375-34.zip'
Content type 'application/zip' length 1217564 bytes (1.2 Mb)
opened URL
downloaded 1.2 Mb

package 'lme4' successfully unpacked and MD5 sums checked

The downloaded packages are in
	C:\WINDOWS\Temp\RtmpV9p1Ho\downloaded_packages

this isn't a Bioconductor issue, as lme4 isn't a BioC package. In 
addition, the bulk of the functionality underlying biocLite() is now 
part of base R.

So I would suggest trying again, and if that doesn't work, try asking on 
R-help. But you might want to give them the results from 
install.packages() rather than biocLite(), lest you get sent back here 
in error.

Best,

Jim


>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>    argument 'lib' is missing: using '/Users/ts/Library/R/2.11/library'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ‘lme4’ is not available
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
>>
>
> Should I be passing in some other parameters too?
>
> thanks,
>
>
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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