Hi everybody, I'm trying to to install and make package hgu133plus2 work on my computer. I run Windows XP. I tried it both with R-2.0.0 and R-2.0.1 and downloaded all packages by default using: >source("http://www.bioconductor.org/getBioC.R") >getBioC() Hgu133plus2 was installed as release package by downloading .zip archive and installing from pull down menu: Install from local zip file(s). Also I tried to install hgu133plus2 as development package using: > library(reposTools) > install.packages2("hgu133plus2", develOK = TRUE) But every time I get following message when type: > hgu133plus2() Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file `C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/hgu133plus2QC.rda' This error causes problems with annotation of my data. Can you suggest something? Thank you very much. Sincerely, Vitalina Komashko.

I have an idea (although I do not know why it is so): R tries to find C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/hgu133plus2QC.rda Inside the directory C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/ you will find a zip file (I think) and if you manually unzip it, and place the .rda file in the data directory, you should be ok. We have seen similar things with other metadat packages under WIndows. I have no idea why, but at least the fix is pretty simple. Kasper On Fri, Feb 25, 2005 at 07:24:41PM -0700, Vitalina Komashko wrote: > Hi everybody, > I'm trying to to install and make package hgu133plus2 work on my computer. I run > Windows XP. > I tried it both with R-2.0.0 and R-2.0.1 and downloaded all packages by default > using: > >source("http://www.bioconductor.org/getBioC.R") > >getBioC() > Hgu133plus2 was installed as release package by downloading .zip archive and > installing from pull down menu: Install from local zip file(s). Also I tried to > install hgu133plus2 as development package using: > > library(reposTools) > > install.packages2("hgu133plus2", develOK = TRUE) > But every time I get following message when type: > > hgu133plus2() > Error in open.connection(con, "rb") : unable to open connection > In addition: Warning message: > cannot open compressed file > `C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/hgu133plus2QC.rda' > This error causes problems with annotation of my data. Can you suggest something? > Thank you very much. > Sincerely, Vitalina Komashko. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen

Hello Kasper, Thank you very much for your reply, it really worked. But now I can't access information from the environments, for example: > id<-ls(env=hgu133plus2ACCNUM) Error in ls(env = hgu133plus2ACCNUM) : Object "hgu133plus2ACCNUM" not found Probably I need to understand where ls(env=xxx) is looking for .rda file. Thank you for your help Best wishes, Vitalina. On Fri Feb 25 22:09 , Kasper Daniel Hansen <k.hansen@biostat.ku.dk> sent: >I have an idea (although I do not know why it is so): R tries to find > >C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/hgu133plus2QC.rda > >Inside the directory > >C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/ > >you will find a zip file (I think) and if you manually unzip it, and >place the .rda file in the data directory, you should be ok. > >We have seen similar things with other metadat packages under WIndows. I >have no idea why, but at least the fix is pretty simple. > >Kasper > >On Fri, Feb 25, 2005 at 07:24:41PM -0700, Vitalina Komashko wrote: >> Hi everybody, >> I'm trying to to install and make package hgu133plus2 work on my computer. I run >> Windows XP. >> I tried it both with R-2.0.0 and R-2.0.1 and downloaded all packages by default >> using: >> >source("http://www.bioconductor.org/getBioC.R") >> >getBioC() >> Hgu133plus2 was installed as release package by downloading .zip archive and >> installing from pull down menu: Install from local zip file(s). Also I tried to >> install hgu133plus2 as development package using: >> > library(reposTools) >> > install.packages2("hgu133plus2", develOK = TRUE) >> But every time I get following message when type: >> > hgu133plus2() >> Error in open.connection(con, "rb") : unable to open connection >> In addition: Warning message: >> cannot open compressed file >> `C:/PROGRA~1/R/rw2000/library/hgu133plus2/data/hgu133plus2QC.rda' >> This error causes problems with annotation of my data. Can you suggest something? >> Thank you very much. >> Sincerely, Vitalina Komashko. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >-- >Kasper Daniel Hansen, Research Assistant >Department of Biostatistics, University of Copenhagen >

Hello James, Thank you very much! I was able to get my IDs! Vitalina. On Sun Feb 27 6:23 , 'James W. MacDonald' jmacdon@med.umich.edu> sent: >Vitalina Komashko wrote: >> Hello Kasper, >> Thank you very much for your reply, it really worked. But now I can't access >> information from the environments, for example: >> >>>id >> >> Error in ls(env = hgu133plus2ACCNUM) : Object "hgu133plus2ACCNUM" not found >> Probably I need to understand where ls(env=xxx) is looking for .rda file. >> Thank you for your help >> Best wishes, Vitalina. >> >There is a slight problem with the way these packages are being built >right now. Until we get this straightened out, you can use this function >to make the package work as expected. > >load.pack > require(package, quietly = TRUE, character.only = TRUE) > files >what = "character", quiet = TRUE) > files > myenv > data(list = files, envir = myenv) >} > >e.g., load.pack("hgu133plus2") > >Note that this will take a while to load considering the size of the >hgu133plus2 package. > >HTH, > >Jim > > > >-- >James W. MacDonald >University of Michigan >Affymetrix and cDNA Microarray Core >1500 E Medical Center Drive >Ann Arbor MI 48109 >734-647-5623 > > > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.