[R] UNC windows path beginning with backslashes: normalizePath bug??

[Uwe Ligges]

This is extremely tricky since Windows does not always accept "//" 
rather than "\\". Additionally, there is not implemented system call in 
Windows, hence ?Sys.glob tells us a "partial emulation" is provided and 
"An attempt is made to handle UNC paths starting with a double backslash."

As you have seenm this does not work everywhere, therefore it is 
advisable to run R from mapped drives - as I am doing in the network of 
our university for 13 years without problems now.

Best,
Uwe Ligges


On 11.08.2011 18:29, Keith Jewell wrote:
> 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.jewell at 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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