On 11/11/2011 07:06 AM, David Iles wrote: > Hi, > > I have experienced similar issues with a number of R packages (not all from BioC - e.g. Rwave; see below) since upgrading to R 2.14 last week. > > A solution would be much appreciated - I'm in the middle of a wavelet analysis! Hi David -- You have a mix of current and outdated packages. One solution might be http://bioconductor.org/install/#update-bioconductor-packages Martin > > Dr David Iles > Institute for Integrative and Comparative Biology > University of Leeds > Leeds LS2 9JT > > d.e.iles at leeds.ac.uk > >> library(Rwave) > Error in library(Rwave) : > package ?Rwave? does not have a NAMESPACE and should be re- installed > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base >> > > > On 11 Nov 2011, at 14:54, Martin Morgan wrote: > >> On 11/11/2011 06:44 AM, James Wagner wrote: >>> Hello, when trying to install these packages using biocLite, I get the >>> messages package "sva" is not available and likewise package >>> "bladderbatch" is not available. With sva I was able to download the tar.gz >>> file and install it using install.packages(), however with bladderbatch I >>> got the message >>> >>> Error : Invalid DESCRIPTION file >>> Package name and namespace differ. >>> >>> The DESCRIPTION file contained the line "namespace auto", which when I >>> removed gave no further errors with the "install.packages()" command, >>> however then when I run library(bladderbatch) I get the warning message: >>> >>> Warning message: >>> In loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = >>> keep.source) : >>> package 'bladderbatch' contains no R code and then with >>> data(bladderbatch) I get that data set 'bladderbatch' not found. >>> >>> What is the best way to hack the DESCRIPTION file to get bladderbatch >>> actually working? >> >> Hi James -- sounds like you are trying to use an incorrect version of R >> (2.13 or before? sva was introduced in the current release). Try >> updating and biocLite() again. Provide sessionInfo() if that doesn't >> sound like the right solution. >> >> Martin >> >>> >>> Thank-you >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793