Hi all

The problem was caused by duplicate \alias entries in a couple of .Rd files, and in fact Herve had already mentioned this. Apologies for missing that. All resolved now.

Thanks
Davis



On Mar 31, 2011, at 10:15 AM, Davis McCarthy wrote:

> 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@wehi.edu.au
> http://www.wehi.edu.au
> 
> 
> 
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:27}}

