Continuing to try to customize my environment for using R under Windoze, I experimented with installing a package from CRAN in a local library ``Lib''. I created the directory ``Lib'' in the folder in which R starts, and then executed > install.packages("abind",lib="Lib") Everything went according to form (I got prompted to choose a mirror, etc.) until the end of the show when I got the warning message Warning: unable to move temporary installation 'C:\Documents and Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\file5f906952\abind to 'C:\Documents and Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\abind' [I have folded the foregoing warning --- which came out as a single line --- to make it fit in an 80 character wide screen.] [I was also told that the ``downloaded packages are in ...'', and when I looked in the indicated folder the zip file was indeed there --- but a fat lot of good that does me.] The warning was more like an *error*. When this had finished, the folder Lib was empty; no sign of the file5f906952 stuff, or anything else. Can anyone explain to me what's going on/wrong? There is no problem apparently if I do > install.packages("abind") which installs into the ``system'' library. In current circumstances this is good enough --- since I have write permission on the ``system'' library, I can just use that. So this is, for the moment, an academic question. Still the facility seems to be *there* for installing to a local user-owned library, and it seems not to be working for me, and I'd like to figure out why. I thought for a moment that I'd found the problem a little while back, when I noticed that ``Lib'' was ``Readonly''. But then when I tried to change that --- ``unclicking'' the Readonly box in the ``Properties'' of Lib --- I found that I couldn't. When I looked at the Properties again, I found it was back to being Readonly again. (With no warning or error message of any kind.) Some further investigation seemed to indicate that *all* folders are Readonly. (Is this really as it should be? And if so, what's the point of having this property for folders?) Can anyone enlighten me? cheers, Rolf Turner rolf at math.unb.ca
This warning is indeed really an error, but do you want all your downloads to fail just because one does? install.packages() behaves the same way on Unices. I was not aware that this works with relative paths for any version of R. Try using a full path, which always works for me. If indeed your filesystem is readonly, you will have problems in spades. But is that box just dark and not ticked? (That's a lovely Windows gotcha that has caught people here many times.) On Fri, 1 Sep 2006, Rolf Turner wrote:> > Continuing to try to customize my environment for using R under > Windoze, I experimented with installing a package from CRAN in a > local library ``Lib''. > > I created the directory ``Lib'' in the folder in which R starts, > and then executed > > > install.packages("abind",lib="Lib") > > Everything went according to form (I got prompted to choose a mirror, > etc.) until the end of the show when I got the warning message > > Warning: unable to move temporary installation 'C:\Documents and > Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\file5f906952\abind to > 'C:\Documents and Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\abind' > > [I have folded the foregoing warning --- which came out as a single line --- > to make it fit in an 80 character wide screen.] > > [I was also told that the ``downloaded packages are in ...'', and when > I looked in the indicated folder the zip file was indeed there --- > but a fat lot of good that does me.] > > The warning was more like an *error*. When this had finished, the folder > Lib was empty; no sign of the file5f906952 stuff, or anything else. > > Can anyone explain to me what's going on/wrong? There is no problem > apparently if I do > > > install.packages("abind") > > which installs into the ``system'' library. In current circumstances > this is good enough --- since I have write permission on the ``system'' > library, I can just use that. So this is, for the moment, an > academic question. Still the facility seems to be *there* for > installing to a local user-owned library, and it seems not to be > working for me, and I'd like to figure out why. > > I thought for a moment that I'd found the problem a little while > back, when I noticed that ``Lib'' was ``Readonly''. But then > when I tried to change that --- ``unclicking'' the Readonly box > in the ``Properties'' of Lib --- I found that I couldn't. When > I looked at the Properties again, I found it was back to being > Readonly again. (With no warning or error message of any kind.) > Some further investigation seemed to indicate that *all* folders > are Readonly. (Is this really as it should be? And if so, what's > the point of having this property for folders?) > > Can anyone enlighten me? > > cheers, > > Rolf Turner > rolf at math.unb.ca > > ______________________________________________ > R-help at stat.math.ethz.ch 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. >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Hi Rolf, Rolf Turner wrote:> Continuing to try to customize my environment for using R under > Windoze, I experimented with installing a package from CRAN in a > local library ``Lib''. > > I created the directory ``Lib'' in the folder in which R starts, > and then executed > > > install.packages("abind",lib="Lib")I don't think this is how you should do things, since R won't know about this library path. Instead, you should use .libPaths() to set your library path and then install using that. Note that you will likely need to put a call to .libPaths() into a .Rprofile file in order to have this set on startup. > dir.create("C:/Documents and Settings/Jim/newlib") > .libPaths("C:/Documents and Settings/Jim/newlib") > install.packages("zoo") Warning in install.packages("zoo") : argument 'lib' is missing: using C:/Documents and Settings/Jim/newlib trying URL 'http://www.biometrics.mtu.edu/CRAN/bin/windows/contrib/2.3/zoo_1.2-0.zip' Content type 'application/zip' length 724426 bytes opened URL downloaded 707Kb package 'zoo' successfully unpacked and MD5 sums checked The downloaded packages are in C:\WINDOWS\Temp\RtmpVcjtqb\downloaded_packages updating HTML package descriptions > dir("C:/Documents and Settings/Jim/newlib") [1] "zoo" Then you can use install.packages("packagename", lib = .libPaths()[2]) if you want to use the 'stock' library directory, or just install.packages("packagename") to use your private one. HTH, Jim> > Everything went according to form (I got prompted to choose a mirror, > etc.) until the end of the show when I got the warning message > > Warning: unable to move temporary installation 'C:\Documents and > Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\file5f906952\abind to > 'C:\Documents and Settings\rolf\My Documents\Rstuff\Lib\file5f906952\Lib\abind' > > [I have folded the foregoing warning --- which came out as a single line --- > to make it fit in an 80 character wide screen.] > > [I was also told that the ``downloaded packages are in ...'', and when > I looked in the indicated folder the zip file was indeed there --- > but a fat lot of good that does me.] > > The warning was more like an *error*. When this had finished, the folder > Lib was empty; no sign of the file5f906952 stuff, or anything else. > > Can anyone explain to me what's going on/wrong? There is no problem > apparently if I do > > > install.packages("abind") > > which installs into the ``system'' library. In current circumstances > this is good enough --- since I have write permission on the ``system'' > library, I can just use that. So this is, for the moment, an > academic question. Still the facility seems to be *there* for > installing to a local user-owned library, and it seems not to be > working for me, and I'd like to figure out why. > > I thought for a moment that I'd found the problem a little while > back, when I noticed that ``Lib'' was ``Readonly''. But then > when I tried to change that --- ``unclicking'' the Readonly box > in the ``Properties'' of Lib --- I found that I couldn't. When > I looked at the Properties again, I found it was back to being > Readonly again. (With no warning or error message of any kind.) > Some further investigation seemed to indicate that *all* folders > are Readonly. (Is this really as it should be? And if so, what's > the point of having this property for folders?) > > Can anyone enlighten me? > > cheers, > > Rolf Turner > rolf at math.unb.ca > > ______________________________________________ > R-help at stat.math.ethz.ch 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.-- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.