Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot find the file specified Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA
Mike Prager wrote:> Windows XP. I have just updated to R 2.11.0 and then run > update.packages. In the series of updates, a few will succeed, then I > get a failure like > > > package 'mvtnorm' successfully unpacked and MD5 sums checked > package 'party' successfully unpacked and MD5 sums checked > package 'PBSmodelling' successfully unpacked and MD5 sums checked > Error in normalizePath(path) : > path[1]="c:\Program Files\R\Library/PBSmodelling": The system cannot > find the file specified >Is that a cut and paste of the error message? Normally R would double the backslashes when displaying a string, so it looks as though you've somehow got a path containing the control characters \P, \R, and \L. Did you set the lib.loc argument when you called update.packages? Duncan Murdoch> > Indeed, the path is missing, though it was there when I issued the > update.packages command. > > ??? > > -- > Mike Prager, NC, USA > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Georgi Boshnakov
2010-May-11 10:35 UTC
[Rd] update.packages fails with directory not found
I posted a similar problem to this list but had no response.
The full email is copied below.
In a nutshell, I traced the message to normalizePath,
which issues it. The directory does not exist because a "move/rename
directory" command, issued at the end of the installation, failed. The
directory you see would have been renamed to the eventual one otherwise.
Since it is the move/rename command which fails on otherwise
(seemingly) successful installation, is it possible to try to copy the
directory when renaming fails and, if successful, inform the user that
a temporary directory has been left behind?
Georgi Boshnakov
Univeristy of Manchester
----------------------------------------------------------------------
Message: 1
Date: Mon, 10 May 2010 00:07:50 -0400
From: Mike Prager <mike.prager at mhprager.com>
To: r-devel at stat.math.ethz.ch
Subject: [Rd] update.packages fails with directory not found
Message-ID: <t81fu5t8gg8crt5nm3h3d3rg6bcg7lri7k at 4ax.com>
Content-Type: text/plain; charset=us-ascii
Windows XP. I have just updated to R 2.11.0 and then run
update.packages. In the series of updates, a few will succeed, then I
get a failure like
package 'mvtnorm' successfully unpacked and MD5 sums checked
package 'party' successfully unpacked and MD5 sums checked
package 'PBSmodelling' successfully unpacked and MD5 sums checked
Error in normalizePath(path) :
path[1]="c:\Program Files\R\Library/PBSmodelling": The system
cannot
find the file specified
Indeed, the path is missing, though it was there when I issued the
update.packages command.
???
--
Mike Prager, NC, USA
------------------------------
----- Forwarded message from georgi.boshnakov at manchester.ac.uk -----
Date: Thu, 18 Feb 2010 10:43:11 +0000
From: Georgi Boshnakov <georgi.boshnakov at manchester.ac.uk>
Subject: install.packages, normalizePath, file permissions
To: r-devel at r-project.org
Dear developers,
I have a small but more or less well defined inquiry. Another, more
general one for which I was not able to find information is towards
the end of this messages. The question seems to be too technical for
R-help, that is why I post it here.
When installing packages (Windows XP), occasionally the installation
does not complete because, it seems, Windows locks some files. I
normally ignore this as a minor annoyance but now I wish to ask
students to install a number of often used packages by sourcing an R
file and this becomes a problem.
Here is an example:
> install.packages( file.path(fp,"fgui_1.0-0.zip" ),
repos=NULL)
Warning in install.packages(file.path(fp, "fgui_1.0-0.zip"), repos =
NULL) :
argument 'lib' is missing: using 'p:/Rpack'
package 'fgui' successfully unpacked and MD5 sums checked
Error in normalizePath(path) :
path[1]="p:\Rpack/fgui": The system cannot find the file specified
The circumstances are difficult to reproduce. For some reason, the
system does not like "fgui" and maybe other packages. The p: drive
above is network attached and and I have read/write access. Here is
the result of traceback.
> traceback()
7: normalizePath(instPath)
6: sprintf(gettext(fmt, domain = domain), ...)
5: gettextf("unable to move temporary installation '%s' to
'%s'",
normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath))
4: warning(gettextf("unable to move temporary installation '%s' to
'%s'",
normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)),
domain = NA, call. = FALSE, immediate. = TRUE)
3: unpackPkg(pkgs[i], pkgnames[i], lib)
2: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, ...)
1: install.packages(file.path(fp, "fgui_1.0-0.zip"), repos = NULL)
The error seems to be thrown by the folloing chunk towards the end of
.install.winbinary():
ret <- file.rename(file.path(tmpDir, curPkg), instPath)
if(!ret)
warning(gettextf("unable to move temporary installation '%s'
to '%s'",
normalizePath(file.path(tmpDir, curPkg)),
normalizePath(instPath)),
domain = NA, call. = FALSE, immediate. = TRUE)
...
Apparently, renaming failed and a message is displayed.
The failure of rename.file may have left the directory specified by
'instPath' non-existent which may cause normalizePath to fail. When
this happens
the message printed is not that of warninig() but the one from
normalizePath() which is uninformative for the user. Maybe an
additional check here would be appropriate and, given that the
installation has been basically successful at this point, even an
attempt to copy the directory after the refusal by Windows to rename
it? I understand of course that the developers have better things to
do than to wrestle with the caprice of Windows.
===Here is a more general enquiry.
I am using R in a statistics course (about 100) students in a computer
cluster where R is installed on a server, students run WindowsXP and
to my understanding the program is run by something called "Zen". It
seems that if a number of students try loading packages, things become
extremely slow and loading fails for some.
The IT services claim that R is the culprit, I am not sure and
certainly part of the problem is related to the slow speed of the
network, but a few problems seem to be related to permissions. I tried
using options(timeout=N) even trying ridiculous values for N but this
did not improve things.
I was not able to trace discussions of such issues and wonder if
somebody has encountered similar problems.
I am about to try ask the students to install some packages in their
area (called p: drive at this Uni) which prompted the first question
above.
Thank you for any suggestions,
Georgi
--
Dr Georgi Boshnakov tel: (+44) (0)161 306 3684
School of Mathematics fax: (+44) (0)161 306 3669
Alan Turing Building 1.125
The University of Manchester email: Georgi.Boshnakov at manchester.ac.uk
Oxford Road
Manchester M13 9PL
UK
----- End forwarded message -----
--
Dr Georgi Boshnakov tel: (+44) (0)161 306 3684
School of Mathematics fax: (+44) (0)161 306 3669
Alan Turing Building 1.125
The University of Manchester email: Georgi.Boshnakov at manchester.ac.uk
Oxford Road
Manchester M13 9PL
UK
Mike, If you have the time and can consistently reproduce this problem you might try using Sysinternal's Process Monitor program to capture the details of what R and other programs were doing in that directory around the time of the problem. http://technet.microsoft.com/en-us/sysinternals/bb896645.aspx I have not used Process Monitor, but have profitably used the older Filemon program and Process Explorer from Sysinternals. They act somewhat like the Linux lsof and strace programs, tracing things at the interface between a program and the operating system. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com> -----Original Message----- > From: r-devel-bounces at r-project.org > [mailto:r-devel-bounces at r-project.org] On Behalf Of Mike Prager > Sent: Tuesday, May 11, 2010 3:21 PM > To: r-devel at stat.math.ethz.ch > Subject: Re: [Rd] update.packages fails with directory not found > > On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch > <murdoch.duncan at gmail.com> wrote: > > >I'd appreciate it if you could check whether the problems remain in > >R-devel, revision 51980 or later. (A build of this revision > should be > >on CRAN by tomorrow, at > >http://cran.r-project.org/bin/windows/base/rdevel.html .) > > > Thanks for trying to fix this. Here is a cut-and-paste [...edited] > from Rgui.exe. Hope it helps. MHP > > > R version 2.12.0 Under development (unstable) (2010-05-11 r51980) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 [...] > > Natural language support but running in an English locale > > [...] > Loading required package: survival > Loading required package: stats > Loading required package: utils > Loading required package: graphics > Loading required package: splines > > Attaching package: 'Hmisc' > [...] > > > update.packages(ask='graphics') > trying URL [...] > downloaded 1.0 Mb > > package 'maps' successfully unpacked and MD5 sums checked > package 'rgl' successfully unpacked and MD5 sums checked > package 'rJava' successfully unpacked and MD5 sums checked > Warning: unable to move temporary installation 'c:\Program > Files\R\Library\file390c7e87\rJava' to 'c:\Program > Files\R\Library\rJava' > package 'strucchange' successfully unpacked and MD5 sums checked > package 'svMisc' successfully unpacked and MD5 sums checked > package 'tkrplot' successfully unpacked and MD5 sums checked > package 'vcd' successfully unpacked and MD5 sums checked > package 'XML' successfully unpacked and MD5 sums checked > package 'zoo' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\mike.prager\Local > Settings\Temp\RtmpyrBgXD\downloaded_packages > Warning message: > In normalizePath(path) : > path[1]="c:\Program Files\R\Library/rJava": The system cannot find > the file specified > > traceback() > No traceback available > > > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >