On 12/20/2010 1:43 PM, Duncan Murdoch wrote:
Yes, I had it open. In this case it was intentional to give a reproducible example in case something had changed in the new version, in other cases I have had to wait for 2 days before I could reinstall a package. It seems the .dll is the one causing the problem, so wouldnt it be possible to test if this file can be unlinked before trying to unlink the complete directory in utils:::unpackPkgZip? Then the package should be left untouched if it is in use, and not partly deleted as today.Jon Olav Skoien wrote:On 12/17/2010 6:22 PM, Duncan Murdoch wrote:On 17/12/2010 11:13 AM, Jon Olav Skoien wrote:Dear list,(R 2.12.0, Windows 7, 64bit)I recently tried to install a new package ("spacetime"), that depends on"sp" among others. I already had the last one installed, but there was probably a newer version on CRAN, so the commandinstall.packages("spacetime")also gave me: also installing the dependencies ‘sp’, ‘zoo’, ‘xts’ sp was already loaded in this session, so installation failed: package 'sp' successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package 'sp' Unfortunately, the warning should rather say: "cannot completely remove prior installation of package 'sp'"R managed to remove most of the prior installation of sp, except for the .dll. I could go on using sp in the existing sessions, but not load the package in a new session or open the help pages. This has happened to meseveral times, and the only solution I have found to this is to close all R-sessions and install the package again. This is normally ok, butthis time I had some long-time computations running in another R-sessionthat I did not want to interrupt. For the next time, is there a way to reinstall a package without interrupting running R-sessions?For me it seems like the cause of the problem could have been solved bychecking if the .dll can be removed before removing the rest of thepackage, by adding something like the following in utils:::unpackPkgZip?if (unlink(paste(instPath,"/libs/x64/sp.dll", sep = "")) != 0) warning("cannot remove...") before ret<- unlink(instPath, recursive = TRUE) (line 95) x64 in the path would have to be changed to something architecture dependent...Could you try out the new 2.12.1 release? I recall hearing that something like this had changed, but I can't spot the NEWS item right now.Duncan MurdochIt seems it didnt change yet...I installed 2.12.1 (on a different computer, still Windows, but Vista and 32 bit), and after installing and loading sp in one session, I opened a new session and got:R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) ............................ > install.packages("sp") Installing package(s) into ‘C:\Users\Jon\Documents/R/win-library/2.12’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session ---provo con l'URL 'http://cran.at.r-project.org/bin/windows/contrib/2.12/sp_0.9-76.zip'Content type 'application/zip' length 997444 bytes (974 Kb) URL aperto downloaded 974 Kb package 'sp' successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package 'sp' The downloaded packages are in C:\Users\Jon\AppData\Local\Temp\RtmpCTJeBk\downloaded_packages > library(sp) Errore in library(sp) : non c'è alcun pacchetto chiamato 'sp' >The error message is the same as earlier, there is no package called "sp", the attempt to install it again removed the old version except for the .dll.JonDid you have it open at the time? Windows won't let open files be removed, so that could have caused the problem. If it's not that, it could be a permissions problem. Have you tried running R as administrator for the install?
I know that it is possible to avoid this problem by not installing a package in use, but 1) it seems only to affect packages with .dll's, so some packages can be reinstalled while in use 2) you dont always know if a dependent package will download a new version of an installed package
Best wishes, Jon ______________________________________________ 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.
