Installation Error with Bioconductor on R
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Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R")biocLite()When I do that, I get the following error:Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor.Will install the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" the command biocLite() installs a number of packages; the above message is NOT an error, but an information message saying that the packages mentioned above are to be installed. Likely these packages are retrieved from the internet and installed on your computer, there should be quite a bit more output before returning to R, or are you saying that R stops working after the message above? Anything that I install after this gives me the same error. I tried uninstalling R 2.7.0 and installing R 2.6.2, and performing the same commands, as above, but the same thing happens.Does anyone have any suggestions?Thanks,A _________________________________________________________________ _WL_Refresh_messenger_062008 [[alternative HTML version deleted]]
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A A ▴ 30
@a-a-2865
Last seen 10.3 years ago
Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on: http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R")biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor.Will install the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that, everything I install after this gives me the same error. I tried uninstalling R 2.7.0 and installing R 2.6.2, and performing the same commands, as above, but the same thing happens.Does anyone have any suggestions? Thanks,A _________________________________________________________________ _WL_Refresh_messenger_062008 [[alternative HTML version deleted]]
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Hi, On Jun 19, 2008, at 10:52 PM, A A wrote: > Hi, I am trying to install Bioconductor onto R version 2.7.0 for > Windows. I installed R, then followed the instructions on: > http://www.bioconductor.org/download, which state that you should > type the following: > > source("http://bioconductor.org/biocLite.R")biocLite() > > When I do that, I get the following error: > > Running biocinstall version 2.2.9 with R version 2.7.0 Your version > of R requires version 2.2 of BioConductor.Will install the following > packages: [1] "affy" "affydata" "affyPLM" > "annaffy" "annotate" [6] "Biobase" "Biostrings" > "DynDoc" "gcrma" "genefilter" [11] "geneplotter" > "hgu95av2.db" "limma" "marray" "matchprobes" [16] > "multtest" "ROC" "vsn" "xtable" > "affyQCReport" > > Anything that, everything I install after this gives me the same > error. I tried uninstalling R 2.7.0 and installing R 2.6.2, and > performing the same commands, as above, but the same thing > happens.Does anyone have any suggestions? > Thanks,A That's not an error, it's just telling you what it's doing. As you let it run, you should see periodic messages telling you that it's saving the downloads in some temp directory (that's what it does on my mac, so I'm guessing windows is the same). When this process finishes, you can then load any of those bioconductor packages and you're good to go. For instance, after it's finished you can type: > library('affy') > openVignette() And you'll see a list of tutorials for the affy package that you can start working through. HTH, -steve
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