Hi James, That worked a treat! Thanks a million for your help, Cheers, Colin On Thu, Feb 12, 2009 at 5:11 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Colin, > > Please don't take things off-list. The intent is that the list archives > might be a useful thing for people to search for answers. > > colin clarke wrote: > >> Hi James, >> >> sessionInfo() >> >> R version 2.8.1 (2008-12-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] pls_2.1-0 affy_1.14.2 affyio_1.10.1 Biobase_2.2.2 >> plsgenomics_1.2-2 MASS_7.2-45 >> >> >> packageDescription("makecdfenv")$V >> [1] "1.20.0" >> >> packageDescription("affy")$V >> [1] "1.14.2" >> > > This is your problem. You have a very out of date version of affy. No idea > how you got such a beast, but using biocLite() to install packages should > make such a thing impossible. > > So biocLite("affy") should get you fixed up. > > Best, > > Jim > > > > >> Thank you, >> >> Colin >> >> >> >> >> On Thu, Feb 12, 2009 at 4:20 PM, James W. MacDonald >> <jmacdon@med.umich.edu>wrote: >> >> Hi Colin, >>> >>> A sessionInfo() would be helpful, as would the output from >>> >>> packageDescription("makecdfenv")$V >>> and >>> packageDescription("affy")$V >>> >>> as this works for me: >>> >>> library(makecdfenv) >>>> >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> 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: affy >>> Loading required package: affyio >>> >>>> sessionInfo() >>>> >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices datasets utils methods >>> [8] base >>> >>> other attached packages: >>> [1] makecdfenv_1.20.0 affyio_1.10.0 affy_1.21.6 Biobase_2.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] preprocessCore_1.4.0 >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> colin clarke wrote: >>> >>> Hi all, >>>> >>>> R is returning the following error when attempting to load the >>>> makecdfenv >>>> >>>> library("makecdfenv") >>>> Error : package 'affy' does not have a name space >>>> Error in as.environment(pos) : >>>> no item called "newtable" on the search list >>>> Error: package/namespace load failed for 'makecdfenv' >>>> >>>> My version info: >>>> >>>> platform i386-pc-mingw32 >>>> arch i386 >>>> os mingw32 >>>> system i386, mingw32 >>>> status >>>> major 2 >>>> minor 8.1 >>>> year 2008 >>>> month 12 >>>> day 22 >>>> svn rev 47281 >>>> language R >>>> version.string R version 2.8.1 (2008-12-22) >>>> >>>> Any help would be greatly appriciated, >>>> >>>> Colin >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@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 >>> Hildebrandt Lab >>> 8220D MSRB III >>> 1150 W. Medical Center Drive >>> Ann Arbor MI 48109-0646 >>> 734-936-8662 >>> >>> >> > -- > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 > [[alternative HTML version deleted]]