[Rd] misfeature: forced file.copy() of a file over itself truncates the file ...

William Dunlap wdunlap at tibco.com
Fri Jan 27 18:47:36 CET 2012

Since the problem can only occur if the 'to' file
exists, a check like
   if (normalizePath(from) == normalizePath(to)) {
      stop("'from' and 'to' files are the same")
(after verifying that 'to', and 'from', exist)
would avoid the problem.

S+ has a function, match.path, that can say if two paths refer to
the same file (on Unixen compare inode and device
numbers, on Windows compare the output of normalizePath),
That avoids automounter/NFS problems like the following.

We have a unix machine has two names, "sea-union" and "seabldlnx3201",
and the /nfs directory contains both names.  At the shell (on a
second Linux machine) we can see they refer to the same place:
   % pwd
   % ls -id usr /nfs/seabldlnx3201/usr /nfs/sea-union/usr
   358337 /nfs/seabldlnx3201/usr/  358337 /nfs/sea-union/usr/  358337 usr/
   % df usr /nfs/seabldlnx3201/usr /nfs/sea-union/usr
   Filesystem           1K-blocks      Used Available Use% Mounted on
   sea-union:/usr        15385888   3526656  11077664  25% /nfs/sea-union/usr
   seabldlnx3201:/usr    15385888   3526656  11077664  25% /nfs/seabldlnx3201/usr
   sea-union:/usr        15385888   3526656  11077664  25% /nfs/sea-union/usr

S+'s match.path also indicates that they are the same   
   S+> getwd()
   [1] "/nfs/sea-union"
   S+> match.path( c("usr", "/nfs/seabldlnx3201/usr"), "/nfs/sea-union/usr")
   [1] 1 1
   (The last indicates that both paths in the first argument match the
   path in the second, as match() does for strings.)
But R's normalizePath() would lead you to think that they are different
   > getwd()
   [1] "/nfs/sea-union"
   > normalizePath(c("usr", "/nfs/seabldlnx3201/usr", "/nfs/sea-union/usr"))
   [1] "/nfs/sea-union/usr"     "/nfs/seabldlnx3201/usr" "/nfs/sea-union/usr"

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 Ben Bolker
> Sent: Friday, January 27, 2012 9:03 AM
> To: r-devel at r-project.org
> Subject: [Rd] misfeature: forced file.copy() of a file over itself truncates the file ...
>   Try this:
>   fn <- "tmp.dat"
>   x <- 1:3
>   dump("x",file=fn)
>   file.info(fn)  ## 9 bytes
>   file.copy(paste("./",fn,sep=""),fn,overwrite=TRUE)
>   file.info(fn)  ## 0 bytes (!!)
>   Normally file.copy() checks and disallows overwriting a file with
> itself, but it only checks whether character string 'from' is the same
> as character string 'to' and not whether the copy refers to the same
> file by different names, so it lets this go ahead.  It then creates a
> new file with the name of 'to' using file.create():
>      'file.create' creates files with the given names if they do not
>      already exist and truncates them if they do.
> This trashes the existing 'from' file (which was not detected).
> file.copy() then happily appends the contents of 'from' (which is now
> empty) to 'to' ...
>   I don't know whether there's any simple way to fix this, or whether
> it's just a case of "don't do that".  It might be worth mentioning in
> the documentation:
>  `file.copy' will normally refuse to copy a file to itself, but in
> cases where the same file is referred to by different names (as in
> copying "/full/path/to/filename" to "filename" in the current working
> directory), it will truncate the file to zero.
>   Now that I write that it really seems like a 'mis-feature'.
>   On a Unix system I would probably compare inodes, but I don't know if
> there's a good system-independent way to test file identity ...
> $ ls -i tmp.dat
> 114080 tmp.dat
> $ ls -i /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat
> 114080 /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat
>   Would normalizePath() work for this ... ?
> > normalizePath("tmp.dat")
> [1] "/mnt/hgfs/bolker/Documents/R/pkgs/r2jags/pkg/tests/tmp.dat"
>    sincerely
>     Ben Bolker
> ______________________________________________
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