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

[Keith Jewell]

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
>
>
>