I am having trouble installing the flowCore package, because of issues with the "rpanel" and "feature" packages, maybe related to TclTk support. Below is my sessionInfo information and more details from the flowCore installation log. I just downloaded R 2.9.0 on April 22, 2009 and installed BioConductor using: source("http://bioconductor.org/biocLite.R") biocLite() biocLite("flowCore") > sessionInfo() R version 2.9.0 (2009-04-17) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.0 Errors with flowCore installation =============================== source("http://bioconductor.org/biocLite.R") biocLite("flowCore") Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: robustbase Loading required package: pcaPP Loading required package: mvtnorm pcaPP 0.1-1 loaded Scalable Robust Estimators with High Breakdown Point (version 0.5-01) Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'feature' ERROR: lazy loading failed for package ‘flowCore’ * Removing ‘/home/jcampbell/programs/R/lib/R/library/flowCore’ The downloaded packages are in ‘/tmp/RtmpWDdduP/downloaded_packages’ Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'rpanel' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'feature' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'flowCore' had non-zero exit status * Installing *source* package ‘rpanel’ ... ** R ** data ** demo ** inst ** preparing package for lazy loading Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error : package 'tcltk' could not be loaded ERROR: lazy loading failed for package ‘rpanel’ * Removing ‘/home/jcampbell/programs/R/lib/R/library/rpanel’ * Installing *source* package ‘feature’ ... ** R ** data ** inst ** preparing package for lazy loading KernSmooth 2.22 installed Copyright M. P. Wand 1997 Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'rpanel' Error : package 'rpanel' could not be loaded ERROR: lazy loading failed for package ‘feature’ * Removing ‘/home/jcampbell/programs/R/lib/R/library/feature’ Thank you, John Campbell [[alternative HTML version deleted]]

Hi John, it seems that you are having a general problem with your TclTk installation on your system. The issue is really the installation of rpanel, which relies on TclTk to be present. rpanel is a dependencies of the feature package, which again is a dependency of flowCore. So in a way the problem is passed down all the way from there. You should install both tcl and tk (on a Debian system try sudo apt-get install tcl tk), recompile R and run biocLite again. Hope that fixes the issue. TclTk is used by many R packages and you might run in a lot of problems without it. Florian John Campbell wrote: > I am having trouble installing the flowCore package, because of issues with > the "rpanel" and "feature" packages, maybe related to TclTk support. Below > is my sessionInfo information and more details from the flowCore > installation log. I just downloaded R 2.9.0 on April 22, 2009 and installed > BioConductor using: > > > source("http://bioconductor.org/biocLite.R") > biocLite() > biocLite("flowCore") > > >> sessionInfo() >> > R version 2.9.0 (2009-04-17) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.9.0 > > > Errors with flowCore installation > =============================== > source("http://bioconductor.org/biocLite.R") > biocLite("flowCore") > > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: robustbase > Loading required package: pcaPP > Loading required package: mvtnorm > pcaPP 0.1-1 loaded > Scalable Robust Estimators with High Breakdown Point (version 0.5-01) > Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : > there is no package called 'feature' > ERROR: lazy loading failed for package ?flowCore? > * Removing ?/home/jcampbell/programs/R/lib/R/library/flowCore? > > The downloaded packages are in > ?/tmp/RtmpWDdduP/downloaded_packages? > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'rpanel' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'feature' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'flowCore' had non-zero exit status > > * Installing *source* package ?rpanel? ... > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error : package 'tcltk' could not be loaded > ERROR: lazy loading failed for package ?rpanel? > * Removing ?/home/jcampbell/programs/R/lib/R/library/rpanel? > * Installing *source* package ?feature? ... > ** R > ** data > ** inst > ** preparing package for lazy loading > KernSmooth 2.22 installed > Copyright M. P. Wand 1997 > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) : > there is no package called 'rpanel' > Error : package 'rpanel' could not be loaded > ERROR: lazy loading failed for package ?feature? > * Removing ?/home/jcampbell/programs/R/lib/R/library/feature? > > Thank you, > John Campbell > > [[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 -- Florian Hahne, PhD Computational Biology Program Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-3148 fhahne at fhcrc.org