Question: latest devel GO package not built in R2.0.0
0
gravatar for Dick Beyer
14.9 years ago by
Dick Beyer1.4k
Dick Beyer1.4k wrote:
I downloaded the latest devel GO package: >From URL: http://www.bioconductor.org/data/metaData-devel/ GO version 1.6.2 but it was built in 1.9.0, so I can't load it in 2.0.0beta. Would someone please build GO for R2.0.0? I am trying to use annaffy for the affy mouse4302 chip, but the mouse4302 meta data is only for R2.0.0. So I think I am stuck. Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
go mouse4302 affy annaffy • 413 views
ADD COMMENTlink modified 14.9 years ago by John Zhang2.9k • written 14.9 years ago by Dick Beyer1.4k
Answer: latest devel GO package not built in R2.0.0
0
gravatar for John Zhang
14.9 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>but it was built in 1.9.0, so I can't load it in 2.0.0beta. Would someone please build GO for R2.0.0? Now, if you do >library(reposTools) >install.packages2("GO", develOK = TRUE) you will get the devel GO package built under R 2.0.0. The package still has a version number 1.6.2 but the GOTERM environment is a list of lists rather than a list of GOTerms objects as it was before (we could not change the version number due to a problem with our CVS). The reason for having a list of lists is to save space as the data packages are getting bigger and bigger. > >I am trying to use annaffy for the affy mouse4302 chip, but the mouse4302 meta data is only for R2.0.0. So I think I am stuck. > >Thanks very much, >Dick >********************************************************************* ********** >Richard P. Beyer, Ph.D. University of Washington >Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 >http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 14.9 years ago by John Zhang2.9k
Hi John, Thanks very much for your reply. I tried doing as you suggested, but I get a new error now. Here is the relevant output: R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.0 beta (2004-09-22), ISBN 3-900051-07-0 > library(reposTools) Loading required package: tools > install.packages2("GO", develOK = TRUE) Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users [1] "Attempting to download GO from http://www.bioconductor.org/data /metaData-devel/" [1] "Download complete." [1] "Installing GO" Note: Running R version 2.0.0 and package GO was built for R version 1.9.0 , installing anyway. [1] "Installation complete" >From URL: http://www.bioconductor.org/data/metaData-devel/ GO version 1.6.2 > library(annaffy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Error: package 'GO' required by 'annaffy' could not be found > local({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Error in library(pkg, character.only = TRUE) : 'GO' is not a valid package -- installed < 2.0.0? Not usre what to try next. Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ********************************************************************** ********* On Fri, 24 Sep 2004, John Zhang wrote: > >> but it was built in 1.9.0, so I can't load it in 2.0.0beta. Would someone > please build GO for R2.0.0? > > Now, if you do > >> library(reposTools) >> install.packages2("GO", develOK = TRUE) > > you will get the devel GO package built under R 2.0.0. The package still has a > version number 1.6.2 but the GOTERM environment is a list of lists rather than a > list of GOTerms objects as it was before (we could not change the version number > due to a problem with our CVS). The reason for having a list of lists is to save > space as the data packages are getting bigger and bigger. > >> >> I am trying to use annaffy for the affy mouse4302 chip, but the mouse4302 meta > data is only for R2.0.0. So I think I am stuck. >> >> Thanks very much, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > >
ADD REPLYlink written 14.9 years ago by Dick Beyer1.4k
Answer: latest devel GO package not built in R2.0.0
0
gravatar for John Zhang
14.9 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>> library(reposTools) >Loading required package: tools >> install.packages2("GO", develOK = TRUE) >Note: You did not specify a download type. Using a default value of: Win32 >This will be fine for almost all users Sorry, we were only able build the GO package under 2.0.0 for unix but not for Windows yet. You may try using a unix machine or wait until next week when our CVS is back. > >[1] "Attempting to download GO from http://www.bioconductor.org/data/metaData-devel/" >[1] "Download complete." >[1] "Installing GO" >Note: Running R version 2.0.0 and package GO was built for R version 1.9.0 > , installing anyway. > >[1] "Installation complete" >>From URL: http://www.bioconductor.org/data/metaData-devel/ > GO version 1.6.2 > >> library(annaffy) >Loading required package: Biobase >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Error: package 'GO' required by 'annaffy' could not be found >> local({pkg <- select.list(sort(.packages(all.available = TRUE))) >+ if(nchar(pkg)) library(pkg, character.only=TRUE)}) >Error in library(pkg, character.only = TRUE) : > 'GO' is not a valid package -- installed < 2.0.0? > >Not usre what to try next. > >Thanks very much, >Dick > >********************************************************************* ********** >Richard P. Beyer, Ph.D. University of Washington >Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 >http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >********************************************************************* ********** > >On Fri, 24 Sep 2004, John Zhang wrote: > >> >>> but it was built in 1.9.0, so I can't load it in 2.0.0beta. Would someone >> please build GO for R2.0.0? >> >> Now, if you do >> >>> library(reposTools) >>> install.packages2("GO", develOK = TRUE) >> >> you will get the devel GO package built under R 2.0.0. The package still has a >> version number 1.6.2 but the GOTERM environment is a list of lists rather than a >> list of GOTerms objects as it was before (we could not change the version number >> due to a problem with our CVS). The reason for having a list of lists is to save >> space as the data packages are getting bigger and bigger. >> >>> >>> I am trying to use annaffy for the affy mouse4302 chip, but the mouse4302 meta >> data is only for R2.0.0. So I think I am stuck. >>> >>> Thanks very much, >>> Dick >>> ********************************************************************** ********* >>> Richard P. Beyer, Ph.D. University of Washington >>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>> Seattle, WA 98105-6099 >>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Jianhua Zhang >> Department of Biostatistics >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> >> > Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 14.9 years ago by John Zhang2.9k
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