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Question: installing BioConductor
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gravatar for Nunez-Garcia, Javier
14.3 years ago by
Nunez-Garcia, Javier20 wrote:
Dear Sir/Madam, I have recently started using R software on a windows 2000 system. I'm trying to install BioConductor but I got the following error message when running getBioC > getBioC() Running getBioC version 1.2.41.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Error in getBioC() : Your R can not connect to the Bioconductor website, which is required for getBioc to work properly. The most likely cause of this is the internet configuration of R > I have also tried to install it from the RGui menu packages but it didn't work neither: > local({a<- CRAN.packages(CRAN=getOption("BIOC")) + install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a, CRAN=getOption("BIOC"))}) trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' unable to resolve 'www.bioconductor.org'. Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"), : cannot open URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' > My internet connection is working fine and I can access to the web sites that R is trying to connect. I have downloaded the packages and tried to install it using the packages menu again but using the option: packages from local zip files, > install.packages(choose.files('',filters=Filters[c('zip','All'),]), .libPaths()[1], CRAN = NULL) Error in file(file, "r") : unable to open connection In addition: Warning messages: 1: error -1 in extracting from zip file 2: cannot open file `Bioconductor/DESCRIPTION' > As well, I can unzip the packages using software such as winzip. Could you please tell me if I'm missing something or if I'm doing something wrong? Many thanks Javi Veterinary Laboratories Agency (VLA) This email and any attachments is intended for the named recipient only. Its unauthorised use, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within VLA systems we can accept no responsibility once it has left our systems. Communications on VLA's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. [[alternative HTML version deleted]]
ADD COMMENTlink modified 14.3 years ago by Jeff Gentry3.9k • written 14.3 years ago by Nunez-Garcia, Javier20
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gravatar for michael watson IAH-C
14.3 years ago by
michael watson IAH-C3.4k wrote:
Hi I think what you need to do is start R thus: Rgui.exe --internet2 Or something similar. If you change your shortcut to point to: "C:\path\to\R\Rgui.exe" --internet2 Then R should be able to access the internet (NOTE the location of the " marks is important) Mick -----Original Message----- From: Nunez-Garcia, Javier [mailto:j.nunez@vla.defra.gsi.gov.uk] Sent: 16 September 2003 10:53 To: 'bioconductor@stat.math.ethz.ch' Subject: [BioC] installing BioConductor Dear Sir/Madam, I have recently started using R software on a windows 2000 system. I'm trying to install BioConductor but I got the following error message when running getBioC > getBioC() Running getBioC version 1.2.41.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Error in getBioC() : Your R can not connect to the Bioconductor website, which is required for getBioc to work properly. The most likely cause of this is the internet configuration of R > I have also tried to install it from the RGui menu packages but it didn't work neither: > local({a<- CRAN.packages(CRAN=getOption("BIOC")) + install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a, CRAN=getOption("BIOC"))}) trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' unable to resolve 'www.bioconductor.org'. Error in download.file(url = paste(contriburl, "PACKAGES", sep = "/"), : cannot open URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' > My internet connection is working fine and I can access to the web sites that R is trying to connect. I have downloaded the packages and tried to install it using the packages menu again but using the option: packages from local zip files, > install.packages(choose.files('',filters=Filters[c('zip','All'),]), .libPaths()[1], CRAN = NULL) Error in file(file, "r") : unable to open connection In addition: Warning messages: 1: error -1 in extracting from zip file 2: cannot open file `Bioconductor/DESCRIPTION' > As well, I can unzip the packages using software such as winzip. Could you please tell me if I'm missing something or if I'm doing something wrong? Many thanks Javi Veterinary Laboratories Agency (VLA) This email and any attachments is intended for the named recipient only. Its unauthorised use, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within VLA systems we can accept no responsibility once it has left our systems. Communications on VLA's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 14.3 years ago by michael watson IAH-C3.4k
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gravatar for Jeff Gentry
14.3 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
> I have also tried to install it from the RGui menu packages but it didn't > work neither: Can you access the CRAN packages from Rgui?
ADD COMMENTlink written 14.3 years ago by Jeff Gentry3.9k
I am new to the bioconductor and just installed the R 1.7.1 and Bioconductor on my WinXP machine. I followed the instruction from chris bye's A Biologist's Guide to using Bioconductor. Everything was fine until I started to export the normalized data. My test project is test.raw. I did load the Biobase, marrayInput, marrayNorm, marrayplot packages. The following is what I copied from R section: > a <- "a" > b <- "b" > test.var <- cbind("a","b") > test.phe <- new("phenoData", varLabels=test.var) Error in validObject(.Object) : Invalid "phenoData" object: Invalid object for slot "varLabels" in class "phenoData": got class "matrix", should be or extend class "list" > Any suggestion? Thanks a lot for your help, Ying Chen
ADD REPLYlink written 14.3 years ago by ying chen40
Hi Ying. I have just update R (1.7.0 to 1.7.1) and also update BioConductor, and I have exacly the same error : With the old version, your code is fine. With the new one, it doesn't work. I don't know how to do correctly the same goal (create phenodata) with the new version (I have just update yesterday), but I hope to have a solution soon. So your problem is not to write code as explain in some documentation, but to know what is the change in the new version (R or bioconductor) L.buffat -----Message d'origine----- De : bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]De la part de ying chen Envoye : mardi 16 septembre 2003 22:10 A : bioconductor@stat.math.ethz.ch Objet : [BioC] Help please! Invalid "phenoData" object I am new to the bioconductor and just installed the R 1.7.1 and Bioconductor on my WinXP machine. I followed the instruction from chris bye's A Biologist's Guide to using Bioconductor. Everything was fine until I started to export the normalized data. My test project is test.raw. I did load the Biobase, marrayInput, marrayNorm, marrayplot packages. The following is what I copied from R section: > a <- "a" > b <- "b" > test.var <- cbind("a","b") > test.phe <- new("phenoData", varLabels=test.var) Error in validObject(.Object) : Invalid "phenoData" object: Invalid object for slot "varLabels" in class "phenoData": got class "matrix", should be or extend class "list" > Any suggestion? Thanks a lot for your help, Ying Chen _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 14.3 years ago by laurent buffat190
Hi again, just as a temporary solution, you can try this code : (I'm suppose you have 4 chips, two factor (a and b) with 2 levels. a <- c("a1","a1","a2","a2") b <- c("b1","b2","b1","b2") covar <- data.frame(a,b) test.phe <- new("phenoData") test.phe@pData <- covar # or pData(test.phe) <- covar test.phe@varLabels <- list(names(covar)) # varLabels(test.phe) <- ... doesn't work. I suppose that is the problem ... L. Buffat -----Message d'origine----- De : bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]De la part de ying chen Envoye : mardi 16 septembre 2003 22:10 A : bioconductor@stat.math.ethz.ch Objet : [BioC] Help please! Invalid "phenoData" object I am new to the bioconductor and just installed the R 1.7.1 and Bioconductor on my WinXP machine. I followed the instruction from chris bye's A Biologist's Guide to using Bioconductor. Everything was fine until I started to export the normalized data. My test project is test.raw. I did load the Biobase, marrayInput, marrayNorm, marrayplot packages. The following is what I copied from R section: > a <- "a" > b <- "b" > test.var <- cbind("a","b") > test.phe <- new("phenoData", varLabels=test.var) Error in validObject(.Object) : Invalid "phenoData" object: Invalid object for slot "varLabels" in class "phenoData": got class "matrix", should be or extend class "list" > Any suggestion? Thanks a lot for your help, Ying Chen _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 14.3 years ago by laurent buffat190
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