Hi Martin,
Sorry I can't fix the update problem. Reading ?browser and ?recover didn't help me out. Finally I uninstalled R, 32/64 bit and RExcel and made a fresh installation of them. Remark: I need to remove all folders with connection to them. Otherwise after installing R, RExcel, rcom, statconnDCOM, R-commander, etc. I still encountered the same problem. After reinstalling above packages ran R as admin, > update.packages() --- Please select a CRAN mirror for use in this session --- cluster : Version 1.13.1 installed in C:/PROGRA~1/R/R-212~1.0/library Version 1.13.2 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y codetools : Version 0.2-2 installed in C:/PROGRA~1/R/R-212~1.0/library Version 0.2-5 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y Matrix : Version 0.999375-44 installed in C:/PROGRA~1/R/R-212~1.0/library Version 0.999375-45 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y mgcv : Version 1.6-2 installed in C:/PROGRA~1/R/R-212~1.0/library Version 1.7-2 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y rpart : Version 3.1-46 installed in C:/PROGRA~1/R/R-212~1.0/library Version 3.1-47 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y survival : Version 2.35-8 installed in C:/PROGRA~1/R/R-212~1.0/library Version 2.36-1 available at http://cran.ms.unimelb.edu.au Update (y/N/c)? y trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/cluster_1.13.2.zip' Content type 'application/zip' length 370152 bytes (361 Kb) opened URL downloaded 361 Kb trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/codetools_0.2-5.zip' Content type 'application/zip' length 42584 bytes (41 Kb) opened URL downloaded 41 Kb trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/Matrix_0.999375-45.zip' Content type 'application/zip' length 3224889 bytes (3.1 Mb) opened URL downloaded 3.1 Mb trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/mgcv_1.7-2.zip' Content type 'application/zip' length 894436 bytes (873 Kb) opened URL downloaded 873 Kb trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/rpart_3.1-47.zip' Content type 'application/zip' length 191611 bytes (187 Kb) opened URL downloaded 187 Kb trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.12/survival_2.36-1.zip' Content type 'application/zip' length 2619051 bytes (2.5 Mb) opened URL downloaded 2.5 Mb package 'cluster' successfully unpacked and MD5 sums checked package 'codetools' successfully unpacked and MD5 sums checked package 'Matrix' successfully unpacked and MD5 sums checked package 'mgcv' successfully unpacked and MD5 sums checked package 'rpart' successfully unpacked and MD5 sums checked package 'survival' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\satimiswin764\AppData\Local\Temp\RtmpM8LYDq\downloaded_packages > Update is now working. Lot of thanks for your detail advice and time spent. 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 10:55:20 AM Subject: Re: [R] Problem on running update On 11/21/2010 05:21 PM, Stephen Liu wrote: > Hi Martin, > > Thanks for your advice. > > This is my first time hunting for cause of error on R. Hi Stephen -- read the help pages ?browser, ?recover *before* trying to use the commands ... > ?browser > ?recover > > 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" [snip] > [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 This says that the error occurred in the .readPkgDesc function; likely one of your package 'DESCRIPTION' files is corrupt. Take a look at the source of .readPkgDesc: > utils:::.readPkgDesc function (lib, fields, pkgs = list.files(lib)) { ret <- matrix(NA_character_, length(pkgs), 2L + length(fields)) for (i in seq_along(pkgs)) { pkgpath <- file.path(lib, pkgs[i]) if (file.access(pkgpath, 5L)) next pkgpath <- file.path(pkgpath, "DESCRIPTION") if (file.access(pkgpath, 4L)) next desc <- tryCatch(read.dcf(pkgpath, fields = fields), error = identity) if (inherits(desc, "error") || NROW(desc) < 1L) { warning(gettextf("read.dcf() error on file '%s'", pkgpath), domain = NA, call. = FALSE) next } desc <- desc[1L, ] Rver <- strsplit(strsplit(desc["Built"], ";")[[1L]][1L], "[ \t]+")[[1L]][2L] desc["Built"] <- Rver ret[i, ] <- c(sub("_.*", "", pkgs[i]), lib, desc) } ret[!is.na(ret[, 1L]), ] } <environment: namespace:utils> you'll end up somewhere in the middle of this code. The variable 'pkgs' will contain a vector of packages, and you'll likely be processing the i'th package. So provoke the error > options(error=recover) > update.packages(repos="http://cran.r-project.org") and when the bug occurs > 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: indicate that you'd like to enter the 5th 'Selection' > Selection: 5 You should see something like Browse[1]> you are 'inside' .readPkgDesc, so you can look around a little, e.g., Browse[1]> pkgs Browse[1]> length(pkgs) Browse[1]> i Browse[1]> pkgs[i] and with a little luck pkgs[i] will be the problem. It'll be located in the directory Browse[1]> lib it would be helpful to look at the content of the DESCRIPTION file, to understand what is wrong Browse[1]> readLines(pkgpath) If 'i' is 1 or length(pkgs) then it might pay to look around some more -- these occur at the start and end of the loop in .readPkgDesc, so you might be having problems in one of the surrounding lines. To fix this, one might quit the browser Browser[1]> Q and quit recover > Selection: 0 and reset how errors are handled > options(error=NULL) and use remove.packages() (see ?remove.packages) to remove the problem package. Alternatively, you might find it necessary to use your operating system to manually remove the directory in which the DESCRIPTION file was found. Include the output of > sessionInfo() to make sure you're using a recent version of R. Here's mine: > sessionInfo() R version 2.12.0 Patched (2010-11-21 r53647) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.12.0 Martin > 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.