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

On 20.12.2010 09:41, 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'? 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.

Which suggests there may be another R session that has the package 
loaded (i.e. the dll locked).

Just close all your R sessions and try again.

Uwe Ligges