R devel - Jul 2013 - Error from R CMD check

Dear all,

I'm puzzled by the error I get from R CMD check one of my packages. I'm
running R CMD check with the --as-cran flag and it get the error both from
running it from the command line as from within Rstudio. On the same machine R
CMD check on my GRTS package (https://r-forge.r-project.org/R/?group_id=1027)
works fine.

Any suggestions on how to fix this? I can send the source code in a private
email if required.

Best regards,

Thierry

Output from Rcmd.exe check --as-cran watervogels_0.3-27.tar.gz


* using log directory 'U:/svn2/watervogels/watervogels.Rcheck'
* using R version 3.0.1 Patched (2013-07-14 r63298)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'watervogels/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'watervogels' version '0.3-27'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Thierry Onkelinx <Thierry.Onkelinx at inbo.be>'
New submission
Non-FOSS package license (Private package of the Research Institute for Nature
and
Forest)
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'watervogels' can be installed ... ERROR
Installation failed.
See 'U:/svn2/watervogels/watervogels.Rcheck/00install.out' for details.

Exited with status 1.



Output from 00install.out

* installing *source* package 'watervogels' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in Sys.junction(from, to) :
  cannot set reparse point
'C:\DOCUME~1\THIERR~2\LOCALS~1\Temp\RtmpMZUCyo\RLIBS_15585fa46d84/watervogels',
reason 'De in de reparsepuntbuffer aanwezige gegevens zijn ongeldig'
Error in flink(normalizePath(pkgdir), tmplib) :
  cannot link from U:\svn2\watervogels\watervogels.Rcheck\00_pkg_src\watervogels
* removing 'U:/svn2/watervogels/watervogels.Rcheck/watervogels'

A translation of the error message: The data in the reparse point buffer are
invalid.

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey


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On 13-07-30 6:34 AM, ONKELINX, Thierry wrote:
> Dear all,
>
> I'm puzzled by the error I get from R CMD check one of my packages.
I'm running R CMD check with the --as-cran flag and it get the error both
from running it from the command line as from within Rstudio. On the same
machine R CMD check on my GRTS package
(https://r-forge.r-project.org/R/?group_id=1027) works fine.
>
> Any suggestions on how to fix this? I can send the source code in a private
email if required.
>
> Best regards,
>
> Thierry
>
> Output from Rcmd.exe check --as-cran watervogels_0.3-27.tar.gz
>
>
> * using log directory 'U:/svn2/watervogels/watervogels.Rcheck'
> * using R version 3.0.1 Patched (2013-07-14 r63298)
> * using platform: i386-w64-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * checking for file 'watervogels/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'watervogels' version '0.3-27'
> * package encoding: UTF-8
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: 'Thierry Onkelinx <Thierry.Onkelinx at inbo.be>'
> New submission
> Non-FOSS package license (Private package of the Research Institute for
Nature and
> Forest)
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'watervogels' can be installed ... ERROR
> Installation failed.
> See 'U:/svn2/watervogels/watervogels.Rcheck/00install.out' for
details.
>
> Exited with status 1.
>
>
>
> Output from 00install.out
>
> * installing *source* package 'watervogels' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Warning in Sys.junction(from, to) :
>    cannot set reparse point
'C:\DOCUME~1\THIERR~2\LOCALS~1\Temp\RtmpMZUCyo\RLIBS_15585fa46d84/watervogels',
reason 'De in de reparsepuntbuffer aanwezige gegevens zijn ongeldig'
> Error in flink(normalizePath(pkgdir), tmplib) :
>    cannot link from
U:\svn2\watervogels\watervogels.Rcheck\00_pkg_src\watervogels
> * removing 'U:/svn2/watervogels/watervogels.Rcheck/watervogels'
>
> A translation of the error message: The data in the reparse point buffer
are invalid.
It's hard to diagnose the cause of the error, but you can avoid the use 
of junctions by setting the environment variable R_WIN_NO_JUNCTIONS to 
some non-empty content, and that might avoid it.

Duncan Murdoch