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... 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]]

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]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Be aware that this package does not pass make check on OS X; there has been some discussion of this on the R-sig-mac list, but I have not paid much attention since I don't use it. Kasper On Tue, Jul 6, 2010 at 7:59 AM, Tim Smith <tim_smith_666 at="" yahoo.com=""> 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... > > 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]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >