Hi,
Back in June I posted the message below, but had no replies. I've made a
little progress since then so this is to update anyone interested (!) and to
ask for comments.
Brief problem statement:
Under Windows, some parts of R don't handle UNC paths beginning with
backslashes. Specifically
a) Sys.glob() fails to find some files breaking (e.g.) Rcmdr plugins
Sys.glob(file.path(.libPaths(), "*/etc/menus.txt"))
fails to find files which are there
b) update.packages(ask='graphics') fails when copying the updates into the
destination folders
In Renviron.site I define the site library with forward slashes, not
backslashes thus...
R_LIBS_SITE=//campden/shares/workgroup/stats/R/library/%v
... but the startup process seems to replace them with forward slashes.
I guess because .libPaths with a 'new' argument calls normalizePath which
changes leading slashes to backslashes, even with winslash="/"
normalizePath("//campden/shares/workgroup/stats/R/library", winslash="/")
[1] "\\\\campden/shares/workgroup/Stats/R/library"
I've corrected (??) this by inserting a line into Rprofile.site
assign(".lib.loc", gsub("\\", "/", .libPaths(), fixed=TRUE),
env=environment(.libPaths))
That seems to fix problem (a) above, which was affecting a number of users.
But have I broken anything else?
I'm still experiencing problem (b).
I'm the only person on site who updates packages so I've mapped a drive
letter (L:) and in my own .Rprofile I have a line
assign(".lib.loc", sub("//campden/shares/workgroup/Stats", "L:",
.libPaths(), ignore.case = TRUE), env=environment(.libPaths))
So that's OK as far as it goes, but it's all a bit messy!
If .libPaths is called with a 'new' argument it will breaks things again.
normalizePath seems to produce paths that don't work with Sys.glob.
I have the feeling I'm being silly and making hard work of all this.
Any comments? Suggestions?
Best regards, and thanks in advance/
Keith Jewell
"Keith Jewell"<k.jew...@campden.co.uk> wrote in message news:...
Hi,
Back in 2010 I had a problem with 'update.packages()', which I worked
around by mapping a drive letter to a UNC path [described in
<http://finzi.psych.upenn.edu/Rhelp10/2010-February/229820.html> but my
current workaround is
assign(".lib.loc", sub("\\\\\\\\Server02/stats", "L:", .libPaths(),
ignore.case = TRUE), env=environment(.libPaths))].
More recently a colleague had problems using the 'FactoMineR' plug in for
the Rcmdr package;
a) directly loading 'RcmdrPlugin.FactoMineR' opened and "crashed" R
Commander;
b) opening R Commander without FactoMiner, the Tools option 'Load Rcmdr
plug-in(s)...' was greyed out.
It transpired that in .libPaths() the path to the library holding
'RcmdrPlugin.FactoMineR' was specified as a UNC address:
\\\\Server02/stats/R/library/2.13>. Mapping a virtual drive letter (e.g.
L:) and specifying the path in .libPaths() as a 'local file system' (LFS)
address<L:/R/library/2.13> fixed the problem.
I contacted Professor Fox (maintainer of Rcmdr) who told me that Rcmdr
finds plug-in packages via the command
plugins<- unlist(lapply(.libPaths(), function(x) Sys.glob(file.path(x,
"*/etc/menus.txt"))))
Because file.path and Sys.glob are both vectorised I think (but am not
certain) that this could be simplified to:
plugins<- Sys.glob(file.path(.libPaths(), "*/etc/menus.txt"))
but that's by the way, the problem seems to lie in Sys.glob under Windows
operating systems.
I note that 'help(Sys.glob)' on my Windows system differs from
<http://finzi.psych.upenn.edu/R/library/base/html/Sys.glob.html>.
The latter says "For precise details, see your system's documentation on
the glob system call. There is a POSIX 1003.2 standard<snip> The rest
of these details are indicative (and based on the POSIX standard)".
On Windows "The glob system call is not part of Windows, and we supply a
partial emulation.<snip> An attempt is made to handle UNC paths starting
with a double backslash" which doesn't really inspire confidence.
This was discussed in a 2009 R-devel thread starting here
<https://stat.ethz.ch/pipermail/r-devel/2009-June/053879.html>, but the
patch proposed in that thread seems not to have been implemented (??).
Trying to avoid Sys.glob in the Rcmdr application I came up with this:
list.files(path=file.path(list.files(path=.libPaths(),
full.names=TRUE), "etc"), pattern="^menus\\.txt$", full.names=TRUE)
It seems to give identical results to Sys.glob for mapped drives, works
with UNC paths in Windows, and seems quite fast.
So my questions relate to diagnosis, prognosis, and prescription (cure?).
1) Diagnosis: Am I correct that my problem(s) originate in the "partial
emulation" of glob in Windows.
2) Prognosis: If so, is there any likelihood that the emulation will
improve in the near future?
3) Prescription: If not:
a) is assign(".lib.loc", sub("\\\\\\\\Server02/stats", "L:", .libPaths(),
ignore.case = TRUE), env=environment(.libPaths))
a reasonable workaround in a specific case?
b) is list.files(path=file.path(list.files(path=.libPaths(),
full.names=TRUE), "etc"), pattern="^menus\\.txt$", full.names=TRUE)
a reasonable replacement for the Sys.glob() construction in Rcmdr? I don't
want to suggest to Prof. Fox an amendment which fixes my problem but
'breaks' it for others!
Thanks in advance,
Keith Jewell
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] datasets grDevices splines graphics stats utils tcltk
[8] tools methods base
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