[R] install.packages() - old version deleted, new version did not install

[Duncan Murdoch]

On 20/12/2010 9:03 AM, Jon Olav Skoien wrote:
> On 12/20/2010 1:43 PM, Duncan Murdoch wrote:
> >  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 command
> >>>>>  install.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 me
> >>>>  several 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, but
> >>>>  this time I had some long-time computations running in another
> >>>>  R-session
> >>>>  that 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 by
> >>>>  checking if the .dll can be removed before removing the rest of the
> >>>>  package, 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 Murdoch
> >>
> >>  It 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.
> >>
> >>  Jon
> >
> >  Did 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?
> 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.

I don't know.  Perhaps we could try to rename the folder; if that fails, 
abort the whole thing.  If that succeeds but something later fails, then 
remove all the new stuff and restore the old folder.  Do you know of a 
better test?

Duncan Murdoch

> 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
>
>
>