From Thierry.ONKELINX at inbo.be  Thu Aug  1 11:18:57 2013
From: Thierry.ONKELINX at inbo.be (ONKELINX, Thierry)
Date: Thu, 1 Aug 2013 09:18:57 +0000
Subject: [Rd] Error from R CMD check
In-Reply-To: <51F7A0EC.4070502@gmail.com>
References: <AA818EAD2576BC488B4F623941DA7427CD31C519@inbomail.inbo.be>
	<51F7A0EC.4070502@gmail.com>
Message-ID: <AA818EAD2576BC488B4F623941DA7427CD31EC63@inbomail.inbo.be>

Dear Duncan,

Thank you for your suggestion. R CMD check is no longer failing to install the package.

Best regards,

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


-----Oorspronkelijk bericht-----
Van: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
Verzonden: dinsdag 30 juli 2013 13:18
Aan: ONKELINX, Thierry
CC: r-devel at r-project.org
Onderwerp: Re: [Rd] Error from R CMD check

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

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[Rd] Error from R CMD check
ONKELINX, Thierry