Synopsis:
I am trying to build and install a package in R, but I have run into a
problem where the file names determine success or failure of the package
installation. I started with a single file containing two class
definitions. This package installs properly. If I split the classes into
two files, the build fails. If I simply change the file name of one file
with no other changes, the build and install then works properly.
This does not seem to be proper behavior. I assume I am doing something
wrong, but I have no idea how to debug or fix this problem. Details are
shown below. I welcome all help and advice!!
Ron
General Information:
R version: 2.8.1
this is an installation of a precomplied version of R
OS: Windows XP PRO SP2
> Sys.getlocale()
[1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"
Details:
In this example, I start with a file named "classSiteResourceCapacity.R"
that contains the defintition of two classes shown below.
file=classSiteResourceCapacity.R
setClass("SiteResourceCapacity",
representation(
site = "character",
siteResource = "character",
studyResource = "character",
capacity = "numeric",
allocation = "matrix",
priority = "matrix"
)
)
setClass("RoleCapacity", representation(loadFactor="numeric"),
contains="SiteResourceCapacity")
The package (containing only this file) works when I run R CMD CHECK or R
CMD INSTALL.
However, when I seperate the classes into two files with the contents shown
below (simply split the file contents, no additional changes), CHECK and
INSTALL now fail as can be seen in the following output.
file=classSiteResourceCapacity.R
setClass("SiteResourceCapacity",
representation(
site = "character",
siteResource = "character",
studyResource = "character",
capacity = "numeric",
allocation = "matrix",
priority = "matrix"
)
)
file=classRoleCapacity.R
setClass("RoleCapacity", representation(loadFactor="numeric"),
contains="SiteResourceCapacity")
C:\TEMP>dir Test\R
Volume in drive C is WINXP
Volume Serial Number is F893-77D5
Directory of C:\TEMP\Test\R
01/08/2009 10:11 AM <DIR> .
01/08/2009 10:11 AM <DIR> ..
01/08/2009 09:54 AM 97 classRoleCapacity.R
01/08/2009 09:55 AM 749 classSiteResourceCapacity.R
2 File(s) 846 bytes
2 Dir(s) 58,195,402,752 bytes free
C:\TEMP>R CMD CHECK Test
* checking for working pdflatex ...pdflatex: not found
NO
* checking for working latex ...latex: not found
NO
* using log directory 'C:/TEMP/Test.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'Test/DESCRIPTION' ... OK
* this is package 'Test' version '0.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'Test' can be installed ... ERROR
Installation failed.
See 'C:/TEMP/Test.Rcheck/00install.out' for details.
C:\TEMP>cat 'C:/TEMP/Test.Rcheck/00install.out'
installing R.css in C:/TEMP/Test.Rcheck
---------- Making package Test ------------
adding build stamp to DESCRIPTION
installing R files
preparing package Test for lazy loading
Error in reconcilePropertiesAndPrototype(name, slots, prototype,
superClasses, :
No definition was found for superclass "SiteResourceCapacity" in the
specification of class "RoleCapacity"
Calls: <Anonymous> ... makeClassRepresentation ->
reconcilePropertiesAndPrototype
Execution halted
make[2]: *** [lazyload] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-Test] Error 2
*** Installation of Test failed ***
Removing 'C:/TEMP/Test.Rcheck/Test'
C:\TEMP>R CMD INSTALL Test
installing to 'c:/PROGRA~1/R/R-2.8.1/library'
---------- Making package Test ------------
adding build stamp to DESCRIPTION
installing R files
preparing package Test for lazy loading
Error in reconcilePropertiesAndPrototype(name, slots, prototype,
superClasses, :
No definition was found for superclass "SiteResourceCapacity" in the
specification of class "RoleCapacity"
Calls: <Anonymous> ... makeClassRepresentation ->
reconcilePropertiesAndPrototype
Execution halted
make[2]: *** [lazyload] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-Test] Error 2
*** Installation of Test failed ***
Removing 'c:/PROGRA~1/R/R-2.8.1/library/Test'
Restoring previous 'c:/PROGRA~1/R/R-2.8.1/library/Test'
Then, if I simply change the name of the file "classSiteResourceCapacity.R"
to "aR" , keeping the file "classRoleCapacity" and with no change to the
contents of either file, the package will then pass the CHECK and INSTALL
properly.
C:\TEMP>dir Test\R
Volume in drive C is WINXP
Volume Serial Number is F893-77D5
Directory of C:\TEMP\Test\R
01/08/2009 10:00 AM <DIR> .
01/08/2009 10:00 AM <DIR> ..
01/08/2009 09:55 AM 749 aR
01/08/2009 09:54 AM 97 classRoleCapacity.R
2 File(s) 846 bytes
2 Dir(s) 58,195,918,848 bytes free
C:\TEMP>R CMD CHECK Test
* checking for working pdflatex ...pdflatex: not found
NO
* checking for working latex ...latex: not found
NO
* using log directory 'C:/TEMP/Test.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'Test/DESCRIPTION' ... OK
* this is package 'Test' version '0.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'Test' 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 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 for missing documentation entries ... WARNING
Undocumented S4 classes:
RoleCapacity SiteResourceCapacity
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
WARNING: There was 1 warning, see
C:/TEMP/Test.Rcheck/00check.log
for details
C:\TEMP>R CMD INSTALL Test
installing to 'c:/PROGRA~1/R/R-2.8.1/library'
---------- Making package Test ------------
adding build stamp to DESCRIPTION
installing R files
preparing package Test for lazy loading
no man files in this package
installing indices
installing help
adding MD5 sums
* DONE (Test)
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