[Bioc-devel] Rd metadata R CMD check warning

[Davis McCarthy]

Hi all

Apologies if this message appears twice.

We have been encountering a strange warning from R CMD check when running it on the latest version of edgeR (2.1.13, release candidate now on Bioconductor devel):

* checking Rd metadata ... WARNING
Error in is.function(FUN) : 'FUN' is missing
Calls: print ... format.check_Rd_metadata -> unlist -> lapply -> match.fun
Execution halted

Full output from R CMD check below. Some googling hasn't shed any light on what's going on here. It occurs on both Windows and Mac machines running R 2. 13 alpha, and has only been present in the last round of changes we made. Unfortunately I can't see any way to determine exactly which *.R or *.Rd file is causing this warning.

Does anyone know what's causing this warning and how to resolve it?

Cheers
Davis

++++++++++++++++++++++++++++++++++++++++++

mac1888:svn.BioCdevel dmccarthy$ R CMD check edgeR
* using log directory ‘/Users/dmccarthy/Documents/svn.BioCdevel/edgeR.Rcheck’
* using R version 2.13.0 alpha (2011-03-19 r54880)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘2.1.13’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package ‘edgeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
Error in is.function(FUN) : 'FUN' is missing
Calls: print ... format.check_Rd_metadata -> unlist -> lapply -> match.fun
Execution halted
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
 Running ‘edgeR-Tests.R’
 Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 Running ‘mseq-Tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
 ‘/Users/dmccarthy/Documents/svn.BioCdevel/edgeR.Rcheck/00check.log’
for details



------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au



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