From murdoch.duncan at gmail.com  Thu Oct 20 21:14:30 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Thu, 20 Oct 2011 15:14:30 -0400
Subject: [Rd] cygwing warming when creating a package in windows
In-Reply-To: <00CCDF26-FA7A-41AB-BBB2-544CBFDDAD0D@gmail.com>
References: <1318949773672-3915660.post@n4.nabble.com>
	<00CCDF26-FA7A-41AB-BBB2-544CBFDDAD0D@gmail.com>
Message-ID: <4EA07316.9010801@gmail.com>

On 20/10/2011 3:06 PM, Joshua Wiley wrote:
> That Cygwin warning is expected on Windows.

It can be suppressed by setting an environment variable named CYGWIN 
with value nodosfilewarning, e.g. by doing this at the command line:

SET CYGWIN=nodosfilewarning

Duncan Murdoch


> You can still build the package and it should be fine, although it looks like the documentation may need a bit of tweaking to pass R CMD check.  2.13.2 is the latest version of R, and I would recommend using it over 2.12.2.  Both for the improvements and because others on this list tend to have the later version so helping is easier.
>
> Cheers,
>
> Josh
>
> On Oct 18, 2011, at 7:56, Alba Martinez-Ruiz<amartine at ucsc.cl>  wrote:
>
> >  Dear All,
> >
> >  I am a beginner creating R packages.  I followed the Leisch (2009) tutorial
> >  and the document ?Writing R Extensions? to write an example.
> >
> >  I installed R 2.12.2 (I also tried R2.13.2),  the last version of Rtools and
> >  the recommended packages in a PC with Windows 7 Home Premium.
> >
> >  I can run  R CMD INSTALL linmod in the command prompt and the R CMD check
> >  linmod. The following outputs are obtained:
> >
> >  * installing *source* package 'linmod' ...
> >  ** R
> >  ** preparing package for lazy loading
> >  ** help
> >  *** installing help indices
> >  ** building package indices ...
> >  ** testing if installed package can be loaded
> >
> >  * DONE (linmod)
> >
> >  * using log directory 'D:/mypkg/linmod.Rcheck'
> >  * using R version 2.12.2 (2011-02-25)
> >  * using platform: i386-pc-mingw32 (32-bit)
> >  * using session charset: ISO8859-1
> >  * checking for file 'linmod/DESCRIPTION' ... OK
> >  * checking extension type ... Package
> >  * this is package 'linmod' version '1.0'
> >  * checking package dependencies ... OK
> >  * checking if this is a source package ... OK
> >  * checking for executable files ... OK
> >  * checking whether package 'linmod' can be installed ... OK
> >  * checking package directory ... OK
> >  * checking for portable file names ... OK
> >  * checking DESCRIPTION meta-information ... OK
> >  * checking top-level files ... OK
> >  * checking index information ... OK
> >  * checking package subdirectories ... OK
> >  * checking R files for non-ASCII characters ... OK
> >  * checking R files for syntax errors ... OK
> >  * checking whether the package can be loaded ... OK
> >  * checking whether the package can be loaded with stated dependencies ... OK
> >  * checking whether the package can be unloaded cleanly ... OK
> >  * checking for unstated dependencies in R code ... OK
> >  * checking S3 generic/method consistency ... OK
> >  * checking replacement functions ... OK
> >  * checking foreign function calls ... OK
> >  * checking R code for possible problems ... OK
> >  * checking Rd files ... OK
> >  * checking Rd metadata ... WARNING
> >  Rd files with duplicated alias 'linmod.default':
> >   linmod.Rd linmod.default.Rd
> >  Rd files with duplicated alias 'linmod.formula':
> >   linmod.Rd linmod.formula.Rd
> >  Rd files with duplicated alias 'print.linmod':
> >   linmod.Rd print.linmod.Rd
> >  Rd files with duplicated alias 'summary.linmod':
> >   linmod.Rd summary.linmod.Rd
> >  * checking Rd cross-references ... WARNING
> >  Unknown package(s) '<pkg>' in Rd xrefs
> >  * checking for missing documentation entries ... OK
> >  * checking for code/documentation mismatches ... OK
> >  * checking Rd \usage sections ... OK
> >  * checking Rd contents ... OK
> >  * checking for unstated dependencies in examples ... OK
> >  * checking examples ... OK
> >  * checking PDF version of manual ... OK
> >  WARNING: There were 2 warnings, see   'D:/my pkg/linmod.Rcheck/00check.log'
> >  for details
> >
> >  I don?t know if it is possible to run R CMD build linmod even though I have
> >  two warning. But if I do it, I get the following cygwin warning:
> >
> >  cygwin warning:
> >  MS-DOS style path detected: D:/mypkg/linmod_1.0.tar
> >  Preferred POSIX equivalent is: /cygdrive/d/mypkg/linmod_1.0.tar
> >  CYGWIN environment variable option ?nodosfilewarning? turns off this
> >  warning.
> >  Consult the user?s guide for more details about POSIX paths:
> >  http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
> >
> >  I am not a Linux expert, and I don?t how to fix this error (I couldn?t find
> >  any help in the manuals or forums, at least for me). Please, any help would
> >  be really appreciated.
> >
> >  Many thanks in advance.
> >
> >  Alba Martinez-Ruiz
> >  -------------------------
> >  Facultad de Ingenier?a
> >  Universidad Cat?lica de la Ssma. Concepci?n
> >  Alonso de Rivera 2850,
> >  C.P. 409-0541 Concepci?n, Chile
> >  Tel: + 0056 41 2345232
> >  Fax: + 0056 41 2345300
> >
> >  --
> >  View this message in context: http://r.789695.n4.nabble.com/cygwing-warming-when-creating-a-package-in-windows-tp3915660p3915660.html
> >  Sent from the R devel mailing list archive at Nabble.com.
> >
> >  ______________________________________________
> >  R-devel at r-project.org mailing list
> >  https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] cygwing warming when creating a package in windows
Duncan Murdoch