[Bioc-devel] Rd metadata R CMD check warning

[Hervé Pagès]

Hi Davis,

On 03/30/2011 08:56 PM, Davis McCarthy wrote:
> 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.

Yes there was a bug in recent R 2.13 that was preventing 'R CMD check'
to display the correct warning message. The bug should be fixed in
R 2.13 beta.

Cheers,
H.

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

Program in Computational Biology
Division of Public Health Sciences
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