Hi Martin, Thanks for your advice.
This is my first time hunting for cause of error on R. Steps performed as follows; > Sys.glob(file.path(.libPaths()[1], "*", "DESCRIPTION")) [1] "C:\\Users\\satimis\\Documents/R/win-library/2.12/Ecdat/DESCRIPTION" [2] "C:\\Users\\satimis\\Documents/R/win-library/2.12/RColorBrewer/DESCRIPTION" [3] "C:\\Users\\satimis\\Documents/R/win-library/2.12/Rglpk/DESCRIPTION" [4] "C:\\Users\\satimis\\Documents/R/win-library/2.12/akima/DESCRIPTION" [5] "C:\\Users\\satimis\\Documents/R/win-library/2.12/bitops/DESCRIPTION" [6] "C:\\Users\\satimis\\Documents/R/win-library/2.12/caTools/DESCRIPTION" [7] "C:\\Users\\satimis\\Documents/R/win-library/2.12/cubature/DESCRIPTION" [8] "C:\\Users\\satimis\\Documents/R/win-library/2.12/degreenet/DESCRIPTION" [9] "C:\\Users\\satimis\\Documents/R/win-library/2.12/ergm/DESCRIPTION" [10] "C:\\Users\\satimis\\Documents/R/win-library/2.12/fBasics/DESCRIPTION" [11] "C:\\Users\\satimis\\Documents/R/win-library/2.12/gam/DESCRIPTION" [12] "C:\\Users\\satimis\\Documents/R/win-library/2.12/gdata/DESCRIPTION" [13] "C:\\Users\\satimis\\Documents/R/win-library/2.12/gplots/DESCRIPTION" [14] "C:\\Users\\satimis\\Documents/R/win-library/2.12/gtools/DESCRIPTION" [15] "C:\\Users\\satimis\\Documents/R/win-library/2.12/kinship/DESCRIPTION" [16] "C:\\Users\\satimis\\Documents/R/win-library/2.12/latentnet/DESCRIPTION" [17] "C:\\Users\\satimis\\Documents/R/win-library/2.12/logspline/DESCRIPTION" [18] "C:\\Users\\satimis\\Documents/R/win-library/2.12/maxLik/DESCRIPTION" [19] "C:\\Users\\satimis\\Documents/R/win-library/2.12/miscTools/DESCRIPTION" [20] "C:\\Users\\satimis\\Documents/R/win-library/2.12/network/DESCRIPTION" [21] "C:\\Users\\satimis\\Documents/R/win-library/2.12/numDeriv/DESCRIPTION" [22] "C:\\Users\\satimis\\Documents/R/win-library/2.12/nws/DESCRIPTION" [23] "C:\\Users\\satimis\\Documents/R/win-library/2.12/rgdal/DESCRIPTION" [24] "C:\\Users\\satimis\\Documents/R/win-library/2.12/rgenoud/DESCRIPTION" [25] "C:\\Users\\satimis\\Documents/R/win-library/2.12/rlecuyer/DESCRIPTION" [26] "C:\\Users\\satimis\\Documents/R/win-library/2.12/rsprng/DESCRIPTION" [27] "C:\\Users\\satimis\\Documents/R/win-library/2.12/sem/DESCRIPTION" [28] "C:\\Users\\satimis\\Documents/R/win-library/2.12/shapes/DESCRIPTION" [29] "C:\\Users\\satimis\\Documents/R/win-library/2.12/slam/DESCRIPTION" [30] "C:\\Users\\satimis\\Documents/R/win-library/2.12/snow/DESCRIPTION" [31] "C:\\Users\\satimis\\Documents/R/win-library/2.12/snowFT/DESCRIPTION" [32] "C:\\Users\\satimis\\Documents/R/win-library/2.12/statmod/DESCRIPTION" [33] "C:\\Users\\satimis\\Documents/R/win-library/2.12/statnet/DESCRIPTION" [34] "C:\\Users\\satimis\\Documents/R/win-library/2.12/tripack/DESCRIPTION" [35] "C:\\Users\\satimis\\Documents/R/win-library/2.12/trust/DESCRIPTION" [36] "C:\\Users\\satimis\\Documents/R/win-library/2.12/tweedie/DESCRIPTION" > > traceback() 5: .readPkgDesc(lib, fields) 4: installed.packages(lib.loc = lib.loc) 3: NROW(instPkgs) 2: old.packages(lib.loc = lib.loc, contriburl = contriburl, method = method, available = available, checkBuilt = checkBuilt) 1: update.packages(repos = "http://cran.r-project.org") Enter a frame number, or 0 to exit > options(error=recover) > update.packages(repos="http://cran.r-project.org") 1: update.packages(repos = "http://cran.r-project.org") 2: old.packages(lib.loc = lib.loc, contriburl = contriburl, method = method, a 3: NROW(instPkgs) 4: installed.packages(lib.loc = lib.loc) 5: .readPkgDesc(lib, fields) Selection: 1 Called from: old.packages(lib.loc = lib.loc, contriburl = contriburl, method = method, available = available, checkBuilt = checkBuilt) Browse[1]> ?browser starting httpd help server ... done Browser[1] ?recover Looked at them and wondered what to do next? B.R. Stephen L ----- Original Message ---- From: Martin Morgan <mtmor...@fhcrc.org> To: Stephen Liu <sati...@yahoo.com> Cc: r-help@r-project.org Sent: Mon, November 22, 2010 1:30:29 AM Subject: Re: [R] Problem on running update On 11/21/2010 03:12 AM, Stephen Liu wrote: > Hi Martin, > > Thanks for your advice. > > Ran following code on R-2.12.0 32bit as admin > >> for(lib in .libPaths()) { > + descs <- Sys.glob(file.path(lib, "*", "DESCRIPTION")) > + sizes <- file.info(descs)$size > + names(sizes) <- descs > + print(sizes[sizes < 100]) > + } > named numeric(0) > named numeric(0) > > Where are the above files? If your problem was as a regular user, then run the above code as regular user not admin. Not sure what 'the above files' are that you are looking for; the 'named numeric(0)' says that no packages have DESCRIPTION files with size < 100; the loop looked in all directories in .libPaths() for a subdirectory with file DESCRIPTION; you can find these by for instance Sys.glob(file.path(.libPaths()[1], "*", "DESCRIPTION")) Your next step is to identify where the error is occurring; you might try update.packages(repos="http://cran.r-project.org") and when the error occurs use traceback() to understand the functions that are being called at the time of the error; the output of traceback() will be helpful to the list, even if not useful to you. The next step is likely to try to identify more precisely where the problem is, e.g., options(error=recover) update.packages(repos="http://cran.r-project.org") and then following the instructions on ?recover and ?browser to more precisely identify the problem. Use options(error=NULL) to turn off recovery when done. Martin > > > B.R. > Stephen L > > > > > ----- Original Message ---- > From: Martin Morgan <mtmor...@fhcrc.org> > To: Stephen Liu <sati...@yahoo.com> > Cc: r-help@r-project.org > Sent: Sun, November 21, 2010 2:10:52 PM > Subject: Re: [R] Problem on running update > > On 11/20/2010 08:56 PM, Stephen Liu wrote: >> Hi folks, >> >> Win 7 64bit >> R 2.12.) >> >> Today on running: >> >>> update.packages() >> Error: subscript out of bounds >> >> Unable to proceed. I have been googling around and couldn't discover the >> cause. Pls help. TIA > > Hi Stephen -- maybe > > https://stat.ethz.ch/pipermail/r-help/2010-November/259912.html > > Martin > >> >> >> B.R. >> Stephen L >> >> >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.