R CMD check not running examples under Windows

-----Original Message-----
From: Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de]
Sent: Tuesday, December 09, 2008 2:03 AM
To: Andy Bunn
Cc: r-devel at r-project.org
Subject: Re: [Rd] R CMD check not running examples under Windows

My suggestion is to submit the package to the win-builder service and
look whether that one checks your example, then you know if it is the
package or your setup that causes the problem.

Uwe, thanks for the tip but the issue is definitely my system - not the package. I've built a skeleton using package.skeleton() and the same phenomenon occurs. Same with checking CRAN packages from source. If it is a problem with my system - how do I go about trouble shooting?

Best,
Uwe Ligges


Andy Bunn wrote:

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\Sys
tem32\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/