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 intend...{{dropped:6}}
[Bioc-devel] Rd metadata R CMD check warning
3 messages · Davis McCarthy, Hervé Pagès
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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
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Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319