installing 'lme4' package fails
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
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]]
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@james-w-macdonald-5106
Last seen 1 day ago
United States
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
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@kasper-daniel-hansen-2979
Last seen 13 months ago
United States
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 >
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