Hello, I am trying to use BioConductor's affy package, but there must be something wrong with the way we have things configured. We are running Solaris8 with R-1.6.1 and I have tried the following without success: ===================================================== cd CELFILES R > library(affy) Error in library(affy) : This is not a valid package -- no DESCRIPTION exists ===================================================== Then I tried this: ===================================================== > setwd("~") > source("getBioC.R") > getBioC(libName = "all") Running getBioC version 1.2.3 .... Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Getting/installing packages reposTools and Biobase" Loading required package: Biobase Welcome to Bioconductor To view some introductory material -- look at our vignettes Simply type: openVignette() to see the available vignettes To read a vignette see the openVignette help page for details Creating a new generic function for "summary" in package Biobase Attaching package `Biobase': The following object(s) are masked from package:base : split summary Note: http://cran.r-project.org/src/contrib does not seem to have a valid repository, skipping [1] "Attempting to download ROC from http://www.bioconductor.org/repository/release1.1/package/Source" trying URL `http://www.bioconductor.org/repository/release1.1/package/Source/.//R OC_1.0.1.tar.gz' Content type `application/x-tar' length 80744 bytes opened URL .......... .......... .......... .......... .......... .......... .......... ........ downloaded 78Kb [1] "Download complete, now installing ..." ERROR: cannot write to or create directory '/usr/local/lib/R/library' Error in file(file, "wb") : unable to open connection In addition: Warning messages: 1: Installation of package ROC had non-zero exit status in: downAndInPkg(lib, repDf[pkgRows, ], repURL, type, versForce = versForce) 2: cannot open file `/usr/local/lib/R/library/liblisting.Rda' ===================================================== I looked for the liblisting file and it is readable - and it looks like I would need write access to /usr/local/lib/R/library for this approach to work so hopefully I can use library(affy) instead. I think we have things set up incorrectly...can anyone suggest some things we might try to get this working? -- Thank you, -susan Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories Bio West 228 University of Arizona Tucson, AZ 85721 (520) 626-2597

On Fri, 3 Jan 2003, Susan J. Miller wrote: > ===================================================== > cd CELFILES > R > > library(affy) > Error in library(affy) : This is not a valid package -- no DESCRIPTION > exists > ===================================================== Am I assuming correctly here that you have package affy installed in directory CELFILES? Or in /usr/local/lib/R/library (from below)? If the former, and if CELFILES is not in your .libPaths() set of locations, that would be a problem. You could try: library(affy,lib.loc("CELFILES")) for instance. > Running getBioC version 1.2.3 .... As an aside, there is a newer version of getBioC which solves some problems, you might want to get that. It wouldn't solve this particular issue, but .... > ERROR: cannot write to or create directory '/usr/local/lib/R/library' > Error in file(file, "wb") : unable to open connection > I looked for the liblisting file and it is readable - and it looks like > I would need write access to /usr/local/lib/R/library for this approach > to work so hopefully I can use library(affy) instead. Sure enough, if you don't have write access to that directory, it won't be able to install the file. You can specify parameter 'destdir' in getBioC to be a location where you *do* have write access to, however. -J

Jeff Gentry wrote: > > On Fri, 3 Jan 2003, Susan J. Miller wrote: > > ===================================================== > > cd CELFILES > > R > > > library(affy) > > Error in library(affy) : This is not a valid package -- no DESCRIPTION > > exists > > ===================================================== > > Am I assuming correctly here that you have package affy installed in > directory CELFILES? Or in /usr/local/lib/R/library (from below)? It is in /usr/local/lib/R/library, which is in .libPaths() so I don't know why I can't load the affy package (it tells me that no DESCRIPTION exists). There is a DESCRIPTION.in file but it looks like the installation failed. > If the former, and if CELFILES is not in your .libPaths() set of > locations, that would be a problem. You could try: > library(affy,lib.loc("CELFILES")) for instance. > > > Running getBioC version 1.2.3 .... I just downloaded this, and I have version 1.2.6. Now when I try to install, it doesn't get past reposTools. It gives a warning about a PDF viewer and then dies: ====================================================================== ======== > getBioC(libName="all") Running getBioC version 1.2.6 .... Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Getting/installing packages reposTools and Biobase" Loading required package: Biobase Note: To manually set your viewer, run the command 'setOptionPdfViewer(<path>), where <path> is a path to a valid PDF viewer program. Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Attaching package `Biobase': The following object(s) are masked from package:base : split Creating a new generic function for "summary" in package reposTools Attaching package `reposTools': The following object(s) are masked from package:base : summary Warning message: No available PDF viewer found on system in: setOptionPdfViewer() > ====================================================================== ======== Any other suggestions for getting Bioconductor installed on Solaris8? -susan