installing bioconductor
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@altiner-ahmet-nihnci-g-1415
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
Hi Ahmet, On 8 Sep 2005, altinera at mail.nih.gov wrote: > As instructed on the FAQ manual, I typed in the following to R 2.1.1 > > > >> source(http://www.bioconductor.org/getBioC.R > <http: www.bioconductor.org="" getbioc.r=""> ) > >> getBioC("affy","release") Is this really what you gave to R or what you are retyping for us? I think you want: source("http://www.bioconductor.org/getBioC.R") getBioC("affy") > > And got back the following message > > > > Running getBioC version 0.8 with R version 2.1.1 > > > > Running biocinstall version 1.2 with R version 2.1.1 > > Error in .readRDS(pfile) : cannot read workspace version 0 written > by R 2.1.1; need R 1.4.0 or newer This is a very strange error message, but given what you've told us about what you entered... Well, perhaps you could try again and let us know if you see the same error. + seth
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@james-w-macdonald-5106
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Try source("http://www.bioconductor.org/biocLite.R") biocLite() Best, Jim >>> "Altiner, Ahmet (NIH/NCI) [G]" <altinera at="" mail.nih.gov=""> 09/08/05 3:12 PM >>> As instructed on the FAQ manual, I typed in the following to R 2.1.1 >source(http://www.bioconductor.org/getBioC.R <http: www.bioconductor.org="" getbioc.r=""> ) >getBioC("affy","release") And got back the following message Running getBioC version 0.8 with R version 2.1.1 Running biocinstall version 1.2 with R version 2.1.1 Error in .readRDS(pfile) : cannot read workspace version 0 written by R 2.1.1; need R 1.4.0 or newer Isn't R 2.1.1 newer than R 1.4.0 ? -Ahmet [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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jon butchar ▴ 50
@jon-butchar-1365
Last seen 7.7 years ago
On Thu, 08 Sep 2005 15:12:39 -0400 "Altiner, Ahmet (NIH/NCI) [G]" <altinera at="" mail.nih.gov=""> wrote: > As instructed on the FAQ manual, I typed in the following to R 2.1.1 > > > > >source(http://www.bioconductor.org/getBioC.R > <http: www.bioconductor.org="" getbioc.r=""> ) > > >getBioC("affy","release") > > > > And got back the following message > > > > Running getBioC version 0.8 with R version 2.1.1 > > > > Running biocinstall version 1.2 with R version 2.1.1 > > Error in .readRDS(pfile) : cannot read workspace version 0 written by R > 2.1.1; need R 1.4.0 or newer > > > > > > Isn't R 2.1.1 newer than R 1.4.0 ? > > > > > > -Ahmet > Hi. I don't know if it's related, but getBioC.R now has a "groupName" specification. After sourcing the file, you could do "> getBioC(groupname="affy")" As James McDonald pointed out with Lite, you should also be able to do the same with getBioC, just "> getBioC()" hth, jon b
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@altiner-ahmet-nihnci-g-1415
Last seen 7.7 years ago
Thanks everyone. I tried both suggestions, still getting error message. Both with BiocLite() (same message -- "Error in .readRDS(pfile) : cannot read workspace version 0 written by R 2.1.1; need R 1.4.0 or newer") and if I use: getBioC(groupname="affy") (which gives the error message ("Error in install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", : unused argument(s) (groupname ...)") any takers? Ahmet -----Original Message----- From: jon butchar [mailto:butchar.2@osu.edu] Sent: Thursday, September 08, 2005 4:32 PM To: bioconductor at stat.math.ethz.ch Cc: Altiner, Ahmet (NIH/NCI) [G] Subject: Re: [BioC] installing bioconductor On Thu, 08 Sep 2005 15:12:39 -0400 "Altiner, Ahmet (NIH/NCI) [G]" <altinera at="" mail.nih.gov=""> wrote: > As instructed on the FAQ manual, I typed in the following to R 2.1.1 > > > > >source(http://www.bioconductor.org/getBioC.R > <http: www.bioconductor.org="" getbioc.r=""> ) > > >getBioC("affy","release") > > > > And got back the following message > > > > Running getBioC version 0.8 with R version 2.1.1 > > > > Running biocinstall version 1.2 with R version 2.1.1 > > Error in .readRDS(pfile) : cannot read workspace version 0 written by R > 2.1.1; need R 1.4.0 or newer > > > > > > Isn't R 2.1.1 newer than R 1.4.0 ? > > > > > > -Ahmet > Hi. I don't know if it's related, but getBioC.R now has a "groupName" specification. After sourcing the file, you could do "> getBioC(groupname="affy")" As James McDonald pointed out with Lite, you should also be able to do the same with getBioC, just "> getBioC()" hth, jon b
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On Fri, 09 Sep 2005 08:03:54 -0400 "Altiner, Ahmet (NIH/NCI) [G]" <altinera at="" mail.nih.gov=""> wrote: > Thanks everyone. > > I tried both suggestions, still getting error message. Both with BiocLite() > (same message -- "Error in .readRDS(pfile) : cannot read workspace version 0 > written by R 2.1.1; need R 1.4.0 or newer") > and if I use: > getBioC(groupname="affy") (which gives the error message ("Error in > install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", : > unused argument(s) (groupname ...)") > > any takers? > > Ahmet > Hi. It's "groupName", not "groupname". This was my idiot error in the previous note, that and the misspelling of James MacDonald's name... Still, it looks like something else might be wrong, possibly with the R installation somehow? Anyhow, I hope that groupName works for you. Take care, jon b
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Seems pretty odd - like you have a defective version of something. What happens if you try to install some other package via the menu (I'm guessing you are on windows - you might want to consult the posting guide for the sorts of information that is helpful e.g. the output of sessionInfo). And should that work, what happens if you download affy and try to install from a local zip file? Best wishes, Robert Altiner, Ahmet (NIH/NCI) [G] wrote: > Thanks everyone. > > I tried both suggestions, still getting error message. Both with BiocLite() > (same message -- "Error in .readRDS(pfile) : cannot read workspace version 0 > written by R 2.1.1; need R 1.4.0 or newer") > and if I use: > getBioC(groupname="affy") (which gives the error message ("Error in > install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", : > unused argument(s) (groupname ...)") > > any takers? > > Ahmet > > > > -----Original Message----- > From: jon butchar [mailto:butchar.2 at osu.edu] > Sent: Thursday, September 08, 2005 4:32 PM > To: bioconductor at stat.math.ethz.ch > Cc: Altiner, Ahmet (NIH/NCI) [G] > Subject: Re: [BioC] installing bioconductor > > On Thu, 08 Sep 2005 15:12:39 -0400 > "Altiner, Ahmet (NIH/NCI) [G]" <altinera at="" mail.nih.gov=""> wrote: > > >>As instructed on the FAQ manual, I typed in the following to R 2.1.1 >> >> >> >> >>>source(http://www.bioconductor.org/getBioC.R >> >><http: www.bioconductor.org="" getbioc.r=""> ) >> >> >>>getBioC("affy","release") >> >> >> >>And got back the following message >> >> >> >>Running getBioC version 0.8 with R version 2.1.1 >> >> >> >>Running biocinstall version 1.2 with R version 2.1.1 >> >>Error in .readRDS(pfile) : cannot read workspace version 0 written by R >>2.1.1; need R 1.4.0 or newer >> >> >> >> >> >>Isn't R 2.1.1 newer than R 1.4.0 ? >> >> >> >> >> >>-Ahmet >> > > > Hi. > > I don't know if it's related, but getBioC.R now has a "groupName" > specification. After sourcing the file, you could do > "> getBioC(groupname="affy")" > > As James McDonald pointed out with Lite, you should also be able to do the > same with getBioC, just > "> getBioC()" > > hth, > > jon b > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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