On 7/6/2010 7:59 AM, Tim Smith wrote:
> I was trying to install the lme4 package, but the installation
fails. Here are my commands and output, alongwith the sessionInfo:
> 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???
> Using R version 2.11.1, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
>  "lme4"
> Please wait...
Although biocLite() will install lme4:
Using R version 2.11.0, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
Content type 'application/zip' length 1217564 bytes (1.2 Mb)
downloaded 1.2 Mb
package 'lme4' successfully unpacked and MD5 sums checked
The downloaded packages are in
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
R-help. But you might want to give them the results from
install.packages() rather than biocLite(), lest you get sent back here
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package ???lme4??? is not available
> R version 2.11.1 (2010-05-31)
>  en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> loaded via a namespace (and not attached):
>  tools_2.11.1
> Should I be passing in some other parameters too?
> [[alternative HTML version deleted]]
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> Bioconductor at stat.math.ethz.ch
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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