R devel - Apr 2011 - R 2.13.0-beta for Windows, file.copy() throws suspicious errors due to default value of copy.mode

While checking packages against R 2.13.0-beta on Windows, I have run into a
few strange error messages related to copying files. The errors all relate
to file.copy() and have the form of:

Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) : 
  'mode' must be of length at least one

After half a day of tinkering, the best reproducible example I can come up
with involves using Roxygen to generate man files for the tikzDevice:

# Install roxygen from CRAN and grab tikzDevice source code
R --vanilla --slave -e "install.packages('roxygen')"
git clone git://github.com/Sharpie/RTikZDevice.git

# Generate documentation, first run succeeds:
R --vanilla --slave -e "require(roxygen); roxygenize('RTikZDevice',
'RTikZDevice.build', overwrite = TRUE)"

Loading required package: roxygen
Loading required package: digest
Writing anyMultibyteUTF8Characters to
RTikZDevice.copy/man/anyMultibyteUTF8Characters.Rd
Warning in parse.name(partitum) :
  No name found for the following expression in RTikZDevice/R/cacheMetrics.R
line 3:
  `NULL . . .'
Writing queryMetricsDictionary to
RTikZDevice.copy/man/queryMetricsDictionary.Rd
...
Writing namespace directives to RTikZDevice.copy/NAMESPACE 
Merging collate directive with RTikZDevice/DESCRIPTION to
RTikZDevice.copy/DESCRIPTION 

# Try running it again, and it bombs:
R --vanilla --slave -e "require(roxygen); roxygenize('RTikZDevice',
'RTikZDevice.build', overwrite = TRUE)"

Loading required package: roxygen
Loading required package: digest
Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) : 
  'mode' must be of length at least one
Calls: roxygenize -> copy.dir -> file.copy -> Sys.chmod
In addition: Warning message:
In file.create(to[okay]) :
  cannot create file
'RTikZDevice.copy/.git/objects/pack/pack-cc0dd1e2622e87f86f8c5a8e617fbf77e253cea1.idx',
reason 'Permission denied'
Execution halted


If I replace all calls to file.copy(...) in the roxygen package with
file.copy(..., copy.mode = FALSE) and reinstall it, then I can regenerate
package documentation all day long without errors. I also get no errors when
I perform the same task with R 2.12.2 on Windows or R 2.13.0-beta on OS X
and Linux.

Maybe roxygenize() is abusing file.copy() somehow, but I find the
"'mode'
must be of length at least one" error suspicious.

Any ideas?

Using:
Windows 7 x86_64
R 2.13.0-beta
Rtools 2.13

-Charlie


-----
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
View this message in context:
http://r.789695.n4.nabble.com/R-2-13-0-beta-for-Windows-file-copy-throws-suspicious-errors-due-to-default-value-of-copy-mode-tp3434559p3434559.html
Sent from the R devel mailing list archive at Nabble.com.

It seems I can reproduce this error under Windows 7 too; it happens
when a file is copied to a directory:
> dir.create('abc')
> file.create('testfile')
[1] TRUE
> file.copy('testfile','testfile2')
[1] TRUE
> file.copy('testfile','abc/')
Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) :
  'mode' must be of length at least one
In addition: Warning message:
In file.create(to[okay]) :
  cannot create file 'abc/', reason 'Permission
denied'
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base


Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Thu, Apr 7, 2011 at 3:59 PM, Sharpie <chuck at sharpsteen.net>
wrote:
> While checking packages against R 2.13.0-beta on Windows, I have run into a
> few strange error messages related to copying files. The errors all relate
> to file.copy() and have the form of:
>
> Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) :
> ?'mode' must be of length at least one
>
> After half a day of tinkering, the best reproducible example I can come up
> with involves using Roxygen to generate man files for the tikzDevice:
>
> # Install roxygen from CRAN and grab tikzDevice source code
> R --vanilla --slave -e "install.packages('roxygen')"
> git clone git://github.com/Sharpie/RTikZDevice.git
>
> # Generate documentation, first run succeeds:
> R --vanilla --slave -e "require(roxygen);
roxygenize('RTikZDevice',
> 'RTikZDevice.build', overwrite = TRUE)"
>
> Loading required package: roxygen
> Loading required package: digest
> Writing anyMultibyteUTF8Characters to
> RTikZDevice.copy/man/anyMultibyteUTF8Characters.Rd
> Warning in parse.name(partitum) :
> ?No name found for the following expression in RTikZDevice/R/cacheMetrics.R
> line 3:
> ?`NULL . . .'
> Writing queryMetricsDictionary to
> RTikZDevice.copy/man/queryMetricsDictionary.Rd
> ...
> Writing namespace directives to RTikZDevice.copy/NAMESPACE
> Merging collate directive with RTikZDevice/DESCRIPTION to
> RTikZDevice.copy/DESCRIPTION
>
> # Try running it again, and it bombs:
> R --vanilla --slave -e "require(roxygen);
roxygenize('RTikZDevice',
> 'RTikZDevice.build', overwrite = TRUE)"
>
> Loading required package: roxygen
> Loading required package: digest
> Error in Sys.chmod(to[okay], file.info(from[okay])$mode, TRUE) :
> ?'mode' must be of length at least one
> Calls: roxygenize -> copy.dir -> file.copy -> Sys.chmod
> In addition: Warning message:
> In file.create(to[okay]) :
> ?cannot create file
>
'RTikZDevice.copy/.git/objects/pack/pack-cc0dd1e2622e87f86f8c5a8e617fbf77e253cea1.idx',
> reason 'Permission denied'
> Execution halted
>
>
> If I replace all calls to file.copy(...) in the roxygen package with
> file.copy(..., copy.mode = FALSE) and reinstall it, then I can regenerate
> package documentation all day long without errors. I also get no errors
when
> I perform the same task with R 2.12.2 on Windows or R 2.13.0-beta on OS X
> and Linux.
>
> Maybe roxygenize() is abusing file.copy() somehow, but I find the
"'mode'
> must be of length at least one" error suspicious.
>
> Any ideas?
>
> Using:
> Windows 7 x86_64
> R 2.13.0-beta
> Rtools 2.13
>
> -Charlie
>
>
> -----
> Charlie Sharpsteen
> Undergraduate-- Environmental Resources Engineering
> Humboldt State University