On Jul 22, 2009, at 10:28 , Duncan Murdoch wrote:
On 7/22/2009 9:10 AM, Kevin R. Coombes wrote:
Hi,
Thanks; that confirms that the problem originates where I thought
it did, and provides a fix from within R.
However, the original problem was that running "Rcmd check" from a
Windows/DOS command prompt on a package on a mounted Samba network
drive fails. The failure occurs because of the file.access call in
"install.R", which appears to get incorrect information from the
operating system. Is it possible to get install.R changed so it
works in this situation?
Of course that's possible, but I'd put it at a low priority. The
right solution here is to fix Samba. A simple workaround is to copy
the package to a non-Samba drive. Since this is not our bug, and it
has a simple workaround, I don't want to put an effort into fixing it.
It *is* our bug - this happens on other drives, too, not just samba
(see my "R CMD check failing due to unreliable file.access() on
Windows" post from 7/2 on R-core about this) - hence your advice is
quite far off. Also note that other tools have no issue finding the
correct flags. I thought this is being worked on (according to that
thread)... I'm not saying that file.access() can be fixed easily
(essentially you have to deal with GetFileSecurityW returning
ERROR_NOT_SUPPORTED and use the GetFileAttributesW result or something
similar instead), but check surely can use the same old reality-based
check that it used before 2.9.0.
Cheers,
Simon
Duncan Murdoch
(Under the philosophy that "it is easier to beg forgiveness than to
ask permission", perhaps install R should just try to create/write
what it wants and only fail iby checking the result rather than
'asking permission"....)
Best,
Kevin
Henrik Bengtsson wrote:
See r-devel thread '[Rd] file.access() on network (mounted) drive on
Windows Vista' on Nov 26, 2008:
http://tolstoy.newcastle.edu.au/R/e5/devel/08/11/0806.html
where it was concluded that file.access() is "not 100%", e.g.
file.access() and file.info() can give different answers.
I added fileAccess(..., safe=TRUE) to R.utils, which imitates
file.access() but relies also on file.info() and file.exists() to
infer the rights. It is still not 100% but (hopefully) closer than
file.access().
/H
On Tue, Jul 21, 2009 at 1:55 PM, Kevin R.
Coombes<krcoom...@mdacc.tmc.edu> wrote:
Hi,
The problem almost certainly has something to do with Samba. We
also have a
NetApp file system, and copying the package source to that drive
and running
Rcmd check from Windows works just fine.
When running the commands from an interactive R session,
file_test returns
TRUE and file.access to test write permission indicates a
failure, even
though that information is incorrect.Here is a session transcript:
-----------------------------------------
getwd()
[1] "n:/krc/Umpire/R-Package"
lib <- "Umpire.Rcheck"
file_test("-d", lib)
[1] TRUE
file.access(lib, 2)
Umpire.Rcheck
-1
dir.create(paste(lib, "testdir", sep='/'))
dir(lib)
[1] "00check.log" "00install.out" "testdir" > sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
----------------------------------------
Again, this all worked (and still works) correctly in 2.8.1.
Kevin
Tony Plate wrote:
This error message looks like it comes from src/library/tools/R/
install.R,
which contains the following test:
if (!.file_test("-d", lib) || file.access(lib, 2L))
stop("ERROR: no permission to install to directory ",
sQuote(lib), call. = FALSE)
The function .file_test() is defined earlier in the same file
(it looks at
file.info(lib)$isdir) and appears to be intended to be the same as
utils:::file_test().
You could start trying to figure out what the problem is by
trying these
calls on the directory in question from an interactive R session.
(They seem to work as intended on my Windows system with a
NetApp file
system mounted on a letter drive.)
-- Tony Plate
Kevin R. Coombes wrote:
Hi,
I have just updated R from version 2.8.1 to version 2.9.1. I
am running
Windows XP Professional, Service Pack 3.
With the update, I decided to update a set of packages that I
maintain by
compiling them for the new version. Everything worked fine
except for one
package. This package is unique (among the six I was working
on) in that is
stored on a UNIX-based file server that is exported to the
Windows network
via Samba. The root of that network path is mapped to drive
"N:" on the
local machine.
'Rcmd check' fails for this package under 2.9.1. The error
message in
'00install.out' is:
"Error: ERROR: no permission to install to directory
'N:/krc/Umpire/R-Package/Umpire.Rcheck'"
'Rcmd check' works for this package under 2.8.1.
'Rcmd check' works for this package if the directory is copied
onto a
local hard drive instead of the network drive.
'Rcmd build' and 'Rcmd build --binary' work under both versions.
It would be nice if someone could figure out what has changed
and fix
it....
Best,
Kevin Coombes
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
