Robert, I seem to be getting nowhere fast. I am having trouble with biocLite. The error message I get below with biocLite(GOstats) I get with any other BioC package I try to install. I have also regularly been getting this message: > update.packages(repos=biocReposList(), dependencies=TRUE) Warning: unable to access index for repository http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5 at the beginning of each session as I have this code as part of my .Rprofile to make sure I keep up to date. Despite this code, which Seth suggested I ignore, I have been getting updates. Perhaps I have a corrupted package somewhere? I would be willing to install all my packages from scratch if that is what it takes. Unfortunately, I have not yet learned how to build from source and am dependent on the Windows binaries. What command would I use to install all of BioC? I used to know it, now I've forgotten and couldn't find it on the website. Mark > setRepositories() > utils:::menuInstallPkgs() Warning: unable to access index for repository http://www.bioconductor.org/bin/windows/contrib/2.5 Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type = type) : no packages were specified > source("http://bioconductor.org/getBioC.R") > > biocLite <- function(pkgs, groupName="lite", ...) + { + if (missing(pkgs)) + getBioC(groupName=groupName, ...) + else + getBioC(pkgs=pkgs, groupName=groupName, ...) + } > biocLite(GOstats) Running getBioC version 0.1.8 with R version 2.5.0 Running biocinstall version 2.0.2 with R version 2.5.0 (under development) Your version of R requires version 2.0 of Bioconductor (under development too). Error in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : object "GOstats" not found sessionInfo() R version 2.5.0 Under development (unstable) (2007-02-09 r40677) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" "methods" "base" other attached packages: RWinEdt limma affy affyio Biobase "1.7-5" "2.9.9" "1.13.14" "1.3.3" "1.13.37" Robert Gentleman wrote: > Hi Mark, > It looks like you were installing GOstats from a local copy, are you > sure that is up to date? One thing you might try is to update all > packages, using update.packages, or to reinstall with biocLite - as I > said, it worked for me > > Again, it is not sufficient to do this for files on your hard disk, you > are going to need updated versions of many of them from the bioc website. > > best wishes > Robert > > Mark W Kimpel wrote: >> Robert, >> >> I deleted GOstats from my R library and re-downloaded the latest GOstats >> Win binary from BioC-devel. I deleted my .Rprofile that was preloading >> some packages like affy. So I had a "virgin" instance of R running. I >> get the same error message. I did not debug this time as it looks like >> the same problem I was having before. >> >> Thanks for your continued help. Below is my output. >> Mark >> >> >> R version 2.5.0 Under development (unstable) (2007-02-09 r40677) >> Copyright (C) 2007 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > utils:::menuInstallLocal() >> package 'GOstats' successfully unpacked and MD5 sums checked >> updating HTML package descriptions >> > require(GOstats) >> Loading required package: GOstats >> Loading required package: graph >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()' or start with 'help(Biobase)'. For details >> on reading vignettes, see the openVignette help page. >> >> Loading required package: GO >> Loading required package: annotate >> Loading required package: RBGL >> Loading required package: Category >> Loading required package: KEGG >> Loading required package: genefilter >> Loading required package: survival >> Loading required package: splines >> Error in expMethods[[i]] <- allMethodLists[ii] : >> more elements supplied than there are to replace >> [1] FALSE >> sessionInfo() >> R version 2.5.0 Under development (unstable) (2007-02-09 r40677) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" "datasets" "methods" "base" >> >> other attached packages: >> Category genefilter survival KEGG RBGL annotate >> GO Biobase graph >> "2.1.15" "1.13.8" "2.31" "1.15.1" "1.11.4" "1.13.6" >> "1.15.1" "1.13.37" "1.13.6" >> > >> >> >> Robert Gentleman wrote: >>> Have you tried to reinstall GOstats? Please, do so, >>> >>> eg >>> >>> biocLite("GOstats") >>> >>> and then >>> library(GOstats) >>> >>> and then report exactly what comes across the screen for all steps, >>> thanks >>> Robert >>> >>> >>> Mark W Kimpel wrote: >>>> GOstats is broken in BioC 2.0, and I think in 1.9. Seth and Robert >>>> are working on a fix but are en-route to New Zealand for a >>>> conference. Can I load affycoretools without one or more >>>> dependencies? I just want to use the venn diagram functions. >>>> >>>> Mark >>> >> > -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

Mark W Kimpel wrote: > Robert, > > I seem to be getting nowhere fast. I am having trouble with biocLite. > The error message I get below with biocLite(GOstats) I get with any > other BioC package I try to install. > > I have also regularly been getting this message: > > > update.packages(repos=biocReposList(), dependencies=TRUE) > Warning: unable to access index for repository > http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5 I do not think that this is related to your current problem - but it indicates that something here needs fixing, but as I said it will be a week or two, since all the worker bees are at a conference. > > at the beginning of each session as I have this code as part of my > .Rprofile to make sure I keep up to date. Despite this code, which Seth > suggested I ignore, I have been getting updates. yes, I am not sure it is a good idea to run that every time you start R. My strategy is to have a working version that I update when 1) I know something has been fixed 2) I know something is broken, and want to see if someone has fixed it (prior to sending a bug report) 3) when I know I have enough time to deal with the issues that may arise in dealing with moving targets such as bioc devel and R devel. > > Perhaps I have a corrupted package somewhere? I would be willing to > install all my packages from scratch if that is what it takes. It may well do. The problem seems to be related to some of the methods and since they have been changing and moving between GOstats, Biobase and Category as we start to figure out what really belongs where, updating anyone of these seems to require updating all. Note the problem you are having (the actual error) is coming from inside an R routine, not a bioc one, and R seems confused - just so we are clear on what the likely cause is > > Unfortunately, I have not yet learned how to build from source and am > dependent on the Windows binaries. I strongly recommend a training course of some sort - and agree with Jim, if it is important to you to live at the bleeding edge, then unfortunately you will often need to do some work to make things function as intended. While this may seem an aside, it really isn't. R is an evolving piece of software, with about 20 independent folks adding and subtracting various parts. Bioconductor is essentially the same - so the notion that in a development version all things will work, is simply not going to be reasonable. I wish it were easier, but, IMHO there are big advantages to the strategy R and BIoc are taking - we are getting better and better performance (next release will be even more dramatic for BioC) > > What command would I use to install all of BioC? I used to know it, now > I've forgotten and couldn't find it on the website. I would do something like: source("http://bioconductor.org/biocLite.R") bioLite("GOstats", "Category") and see if that fixes your problem best wishes Robert > > Mark > > > setRepositories() > > utils:::menuInstallPkgs() > Warning: unable to access index for repository > http://www.bioconductor.org/bin/windows/contrib/2.5 > Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type > = type) : > no packages were specified > > source("http://bioconductor.org/getBioC.R") > > > > biocLite <- function(pkgs, groupName="lite", ...) > + { > + if (missing(pkgs)) > + getBioC(groupName=groupName, ...) > + else > + getBioC(pkgs=pkgs, groupName=groupName, ...) > + } > > biocLite(GOstats) > Running getBioC version 0.1.8 with R version 2.5.0 > Running biocinstall version 2.0.2 with R version 2.5.0 (under development) > Your version of R requires version 2.0 of Bioconductor (under > development too). > Error in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > object "GOstats" not found > > sessionInfo() > R version 2.5.0 Under development (unstable) (2007-02-09 r40677) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" > "methods" "base" > > other attached packages: > RWinEdt limma affy affyio Biobase > "1.7-5" "2.9.9" "1.13.14" "1.3.3" "1.13.37" > > > Robert Gentleman wrote: >> Hi Mark, >> It looks like you were installing GOstats from a local copy, are you >> sure that is up to date? One thing you might try is to update all >> packages, using update.packages, or to reinstall with biocLite - as I >> said, it worked for me >> >> Again, it is not sufficient to do this for files on your hard disk, >> you are going to need updated versions of many of them from the bioc >> website. >> >> best wishes >> Robert >> >> Mark W Kimpel wrote: >>> Robert, >>> >>> I deleted GOstats from my R library and re-downloaded the latest GOstats >>> Win binary from BioC-devel. I deleted my .Rprofile that was >>> preloading some packages like affy. So I had a "virgin" instance of R >>> running. I get the same error message. I did not debug this time as >>> it looks like the same problem I was having before. >>> >>> Thanks for your continued help. Below is my output. >>> Mark >>> >>> >>> R version 2.5.0 Under development (unstable) (2007-02-09 r40677) >>> Copyright (C) 2007 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> > utils:::menuInstallLocal() >>> package 'GOstats' successfully unpacked and MD5 sums checked >>> updating HTML package descriptions >>> > require(GOstats) >>> Loading required package: GOstats >>> Loading required package: graph >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()' or start with 'help(Biobase)'. For details >>> on reading vignettes, see the openVignette help page. >>> >>> Loading required package: GO >>> Loading required package: annotate >>> Loading required package: RBGL >>> Loading required package: Category >>> Loading required package: KEGG >>> Loading required package: genefilter >>> Loading required package: survival >>> Loading required package: splines >>> Error in expMethods[[i]] <- allMethodLists[ii] : >>> more elements supplied than there are to replace >>> [1] FALSE >>> sessionInfo() >>> R version 2.5.0 Under development (unstable) (2007-02-09 r40677) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] "splines" "tools" "stats" "graphics" "grDevices" >>> "utils" "datasets" "methods" "base" >>> >>> other attached packages: >>> Category genefilter survival KEGG RBGL annotate >>> GO Biobase graph >>> "2.1.15" "1.13.8" "2.31" "1.15.1" "1.11.4" "1.13.6" >>> "1.15.1" "1.13.37" "1.13.6" >>> > >>> >>> >>> Robert Gentleman wrote: >>>> Have you tried to reinstall GOstats? Please, do so, >>>> >>>> eg >>>> >>>> biocLite("GOstats") >>>> >>>> and then >>>> library(GOstats) >>>> >>>> and then report exactly what comes across the screen for all steps, >>>> thanks >>>> Robert >>>> >>>> >>>> Mark W Kimpel wrote: >>>>> GOstats is broken in BioC 2.0, and I think in 1.9. Seth and Robert >>>>> are working on a fix but are en-route to New Zealand for a >>>>> conference. Can I load affycoretools without one or more >>>>> dependencies? I just want to use the venn diagram functions. >>>>> >>>>> Mark >>>> >>> >> > -- 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

Bingo, that did it. For the record, the link below provides a loadable Win binary of the most current GOStats James W. MacDonald wrote: > Errr. Try > > http://www.umich.edu/~jmacdon/GOstats_2.1.11.zip > > Best, > > Jim > >