[R] Dispatch issue in package check?

Szumiloski, John John.Szumiloski at bms.com
Tue Apr 12 13:51:43 CEST 2016 

Dear useRs,

I am developing a package using RStudio and roxygen markup files.  I have run into a problem while checking.

The relevant function is a generic S3 statistical function modeled on t.test(), with methods.  It returns an object of class "htest" etc.  Here Is the (anonymized) relevant code:

                <...>
#' @examples
#' foo(c(5,4,6,5,7,9,8,11,12,10), <other arguments>)
                <...>
#' @export
foo <- function(x, ...) UseMethod("foo ")
#'
foo.default <- function(x, <other specific arguments>)  {< code adapted from t.test.default() >}
#'
foo.formula <- function(formula, data, subset, na.action, ...) {< code adapted from t.test.formula() >)

The issue comes when checking.  In RStudio I select the Check button in the Build tab.  It executes the command


devtools::check(cleanup = FALSE)

I attach the console output to demonstrate the error, as well as to perhaps see any clues:


Updating <pkg> documentation

Loading <pkg>

Writing NAMESPACE

Writing <Rd files...>

Writing foo.Rd

Writing <Rd files...>

Setting env vars ---------------------------------------------------------------

CFLAGS  : -Wall -pedantic

CXXFLAGS: -Wall -pedantic

Building <pkg> ---------------------------------------------------------------

"C:/PROGRA~1/R/R-32~1.4/bin/i386/R" --no-site-file --no-environ --no-save  \

  --no-restore --quiet CMD build "C:\Users\szumiloj\R\<pkg>"  \

  --no-resave-data --no-manual



* checking for file 'C:\Users\szumiloj\R\<pkg>/DESCRIPTION' ... OK

* preparing '<pkg>':

* checking DESCRIPTION meta-information ... OK

* checking for LF line-endings in source and make files

* checking for empty or unneeded directories

* building '<pkg>_0.0.0.9001.tar.gz'



Setting env vars ---------------------------------------------------------------

_R_CHECK_CRAN_INCOMING_ : FALSE

_R_CHECK_FORCE_SUGGESTS_: FALSE

Checking <other arguments>) ---------------------------------------------------------------

"C:/PROGRA~1/R/R-32~1.4/bin/i386/R" --no-site-file --no-environ --no-save  \

  --no-restore --quiet CMD check  \

  "C:\Users\szumiloj\AppData\Local\Temp\RtmpWKHu33/<pkg>_0.0.0.9001.tar.gz"  \

  --as-cran --timings --no-manual



* using log directory 'C:/Users/szumiloj/R/<pkg>.Rcheck'

* using R version 3.2.4 (2016-03-10)

* using platform: i386-w64-mingw32 (32-bit)

* using session charset: ISO8859-1

* using options '--no-manual --as-cran'

* checking for file '<pkg>/DESCRIPTION' ... OK

* checking extension type ... Package

* this is package '<pkg>' version '0.0.0.9001'

* checking package namespace information ... OK

* checking package dependencies ... OK

* checking if this is a source package ... OK

* checking if there is a namespace ... OK

* checking for executable files ... OK

* checking for hidden files and directories ... OK

* checking for portable file names ... OK

* checking whether package '<pkg>' can be installed ... OK

* checking installed package size ... OK

* checking package directory ... OK

* checking DESCRIPTION meta-information ... OK

* checking top-level files ... OK

* checking for left-over 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 whether the namespace can be loaded with stated dependencies ... OK

* checking whether the namespace can be unloaded cleanly ... OK

* checking loading without being on the library search path ... OK

* checking 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 ... OK

* checking Rd line widths ... OK

* checking Rd cross-references ... OK

* 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 ... ERROR

Running examples in '<pkg>-Ex.R' failed

The error most likely occurred in:



> base::assign(".ptime", proc.time(), pos = "CheckExEnv")

> ### Name: foo

> ### Title: <foo title>

> ### Aliases: foo foo.default foo.formula <"Foo" etc>

>

> ### ** Examples

>

> foo(c(5,4,6,5,7,9,8,11,12,10), <other arguments>)

Error in UseMethod("foo") :

  no applicable method for 'foo' applied to an object of class "c('double', 'numeric')"

Calls: foo

Execution halted

* DONE

Status: 1 ERROR



See

  'C:/Users/szumiloj/R/<pkg>.Rcheck/00check.log'

for details.



checking examples ... ERROR

Running examples in '<pkg>-Ex.R' failed

The error most likely occurred in:



> base::assign(".ptime", proc.time(), pos = "CheckExEnv")

> ### Name: foo

> ### Title: <foo title>

> ### Aliases: foo foo.default foo.formula <"Foo" etc>

>

> ### ** Examples

>

> foo(c(5,4,6,5,7,9,8,11,12,10), <other arguments>)

Error in UseMethod("foo") :

  no applicable method for 'foo' applied to an object of class "c('double', 'numeric')"

Calls: foo

Execution halted

R CMD check results

1 error  | 0 warnings | 0 notes

Warning messages:

1: `cleanup` is deprecated

2: @title [foo.R#1]: requires a value

3: @description [foo.R#1]: requires a value

4: @title [foo.R#1]: requires a value

5: @description [foo.R#1]: requires a value



R CMD check succeeded

It appears to me there is a dispatch problem, that the default method is not being called.  The issue persists even if I @export the default and formula methods.

However, if I source() the whole file foo.Rd into the global environment, then run the example foo(c(5,4,6,5,7,9,8,11,12,10), <other arguments>), it runs just fine.

Any insight as to what is happening here?  Also I do not understand the warnings about @title and @description, as I certainly have those fields in the source file.  But this is not as critical.

Thanks in advance,
John Szumiloski

######## session info


> version

               _

platform       i386-w64-mingw32

arch           i386

os             mingw32

system         i386, mingw32

status

major          3

minor          2.4

year           2016

month          03

day            10

svn rev        70301

language       R

version.string R version 3.2.4 (2016-03-10)

nickname       Very Secure Dishes

> devtools::session_info()

Session info --------------------------------------------------------------------------------

 setting  value

 version  R version 3.2.4 (2016-03-10)

 system   i386, mingw32

 ui       RStudio (0.99.893)

 language (EN)

 collate  English_United States.1252

 tz       America/New_York

 date     2016-04-12



Packages ------------------------------------------------------------------------------------

 package  * version date       source

 devtools * 1.11.0  2016-04-12 CRAN (R 3.2.4)

 digest     0.6.9   2016-01-08 CRAN (R 3.2.3)

 magrittr   1.5     2014-11-22 CRAN (R 3.2.0)

 memoise    1.0.0   2016-01-29 CRAN (R 3.2.3)

 Rcpp       0.12.4  2016-03-26 CRAN (R 3.2.4)

 roxygen2 * 5.0.1   2015-11-11 CRAN (R 3.2.2)

 stringi    1.0-1   2015-10-22 CRAN (R 3.2.2)

 stringr    1.0.0   2015-04-30 CRAN (R 3.2.0)

 withr      1.0.1   2016-02-04 CRAN (R 3.2.3)


John Szumiloski, Ph.D.
Senior Principal Scientist, Statistician
Analytical and Bioanalytical Operations<http://teams.bms.com/sites/ARD/>
NBR105-1-1411

Bristol-Myers Squibb
P.O. Box 191
1 Squibb Drive
New Brunswick, NJ
08903-0191
USA
(732) 227-7167
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