R devel - Oct 2011 - cygwing warming when creating a package in windows

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

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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.

That. Cygwin warning is expected on Windows.  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