From Andy.Bunn at wwu.edu  Mon Dec  8 19:28:42 2008
From: Andy.Bunn at wwu.edu (Andy Bunn)
Date: Mon, 8 Dec 2008 10:28:42 -0800
Subject: [Rd] R CMD check not running examples under Windows
Message-ID: <366AA6C6662BAB4796FF54F8D8BFC74202B7973647@ExchMailbox1.univ.dir.wwu.edu>

All, 


I have a fresh build of R 2.8.0 from source on Windows XP using the latest Rtools binary (Rtools29.exe). All appears to be well with the install and make check-all exits cleanly. However, when running R CMD check mypkg the program jumps from checking for non-ASCII to checking the PDF version of the manual:

* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK

It skips the making the R-ex subdir and checking the examples. Here is the complete log:


* using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
* using R version 2.8.0 (2008-10-20)
* using session charset: ISO8859-1
* checking for file 'dplR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dplR' version '1.1.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'dplR' 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK

I am running this with no flags yet it seems like I'm outside this line in the check script:
  if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {

Here is the version:
> version
               _                           
platform       i386-pc-mingw32             
arch           i386                        
os             mingw32                     
system         i386, mingw32               
status                                     
major          2                           
minor          8.0                         
year           2008                        
month          10                          
day            20                          
svn rev        46754                       
language       R                           
version.string R version 2.8.0 (2008-10-20)
>


And the PATH:
C:\Data\research\dplR_dev>PATH
PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-2.8.0\bin\;C:\P
rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX 2.6\miktex\bin;C:\cygwi
n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbe
m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program Files\Novel
l\ZENworks\;C:\Program Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder Office 3.10;C:\
dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH Communications Sec
urity\SSH Secure Shell;Z:.;

I expect some cygwin or perl issue but I'm not sure how to proceed in tracking this down. Cygwin is a fresh install as well. Any suggestions on what to do next greatly appreciated.

-A

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Andy Bunn
Environmental Sciences, Huxley College
Western Washington University
Bellingham, WA 98225-9181
Skype: andy.bunn
Phone: 360-650-4252
Fax: 360-650-7284
http://myweb.facstaff.wwu.edu/bunna/



[Rd] R CMD check not running examples under Windows
Andy Bunn