Hi the list, I build a package. They was a mistake in it, but R CMD check did not find it. Is that normal ? Here is what Kurt gets (which is right, I did this mistake): --- 8< ---------------- * checking for code/documentation mismatches ... WARNING S4 class codoc mismatches from documentation object 'LongData-class': Slots for class 'LongData' Code: id other time traj varName Docs: id time traj varName --- 8< ---------------- But here is what I get : --- 8< ---------------- R CMD check longitudinalData * checking for working pdflatex ... OK * using log directory 'C:/Documents and Settings/Christophe/Mes documents/Recher che/Trajectoires/kmeal/longitudinalData.Rcheck' * using R version 2.9.0 beta (2009-04-04 r48290) * using session charset: ISO8859-1 * checking for file 'longitudinalData/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'longitudinalData' version '0.5' * package encoding: latin1 * checking package dependencies ... OK * checking if this is a source package ... OK * checking for .dll and .exe files ... OK * checking whether package 'longitudinalData' can be installed ... OK * checking package directory ... OK * checking for portable file names ... 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 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 files against version 2 parser ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking examples ... OK * checking PDF version of manual ... OK R CMD build longitudinalData * checking for file 'longitudinalData/DESCRIPTION' ... OK * preparing 'longitudinalData': * checking DESCRIPTION meta-information ... OK * removing junk files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'longitudinalData_0.5.tar.gz' --- 8< ---------------- Christophe
"using R version 2.9.0 beta (2009-04-04 r48290)" As a start, Kurt et al. are for sure using a much more recent version (probably also the very latest patched version). /H On Tue, Jun 9, 2009 at 7:17 AM, Christophe Genolini<cgenolin at u-paris10.fr> wrote:> Hi the list, > > I build a package. They was a mistake in it, but R CMD check did not find > it. Is that normal ? > > Here is what Kurt gets (which is right, I did this mistake): > > --- 8< ---------------- > * checking for code/documentation mismatches ... WARNING > S4 class codoc mismatches from documentation object 'LongData-class': > Slots for class 'LongData' > ?Code: id other time traj varName > ?Docs: id time traj varName > --- 8< ---------------- > > But here is what I get : > > --- 8< ---------------- > R CMD check longitudinalData > * checking for working pdflatex ... OK > * using log directory 'C:/Documents and Settings/Christophe/Mes > documents/Recher > che/Trajectoires/kmeal/longitudinalData.Rcheck' > * using R version 2.9.0 beta (2009-04-04 r48290) > * using session charset: ISO8859-1 > * checking for file 'longitudinalData/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'longitudinalData' version '0.5' > * package encoding: latin1 > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking for .dll and .exe files ... OK > * checking whether package 'longitudinalData' can be installed ... OK > * checking package directory ... OK > * checking for portable file names ... 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 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 files against version 2 parser ... OK > * checking Rd cross-references ... OK > * checking for missing documentation entries ... OK > * checking for code/documentation mismatches ... OK > * checking Rd \usage sections ... OK > * checking examples ... OK > * checking PDF version of manual ... OK > > > R CMD build longitudinalData > * checking for file 'longitudinalData/DESCRIPTION' ... OK > * preparing 'longitudinalData': > * checking DESCRIPTION meta-information ... OK > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'longitudinalData_0.5.tar.gz' > --- 8< ---------------- > > Christophe > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
try issueing this before calling R CMD check export _R_CHECK_CODOC_S4_METHODS_=true hth, Ingmar On 9 Jun 2009, at 16:17, Christophe Genolini wrote:> Hi the list, > > I build a package. They was a mistake in it, but R CMD check did not > find it. Is that normal ? > > Here is what Kurt gets (which is right, I did this mistake): > > --- 8< ---------------- > * checking for code/documentation mismatches ... WARNING > S4 class codoc mismatches from documentation object 'LongData-class': > Slots for class 'LongData' > Code: id other time traj varName > Docs: id time traj varName > --- 8< ---------------- > > But here is what I get : > > --- 8< ---------------- > R CMD check longitudinalData > * checking for working pdflatex ... OK > * using log directory 'C:/Documents and Settings/Christophe/Mes > documents/Recher > che/Trajectoires/kmeal/longitudinalData.Rcheck' > * using R version 2.9.0 beta (2009-04-04 r48290) > * using session charset: ISO8859-1 > * checking for file 'longitudinalData/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'longitudinalData' version '0.5' > * package encoding: latin1 > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking for .dll and .exe files ... OK > * checking whether package 'longitudinalData' can be installed ... OK > * checking package directory ... OK > * checking for portable file names ... 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 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 files against version 2 parser ... OK > * checking Rd cross-references ... OK > * checking for missing documentation entries ... OK > * checking for code/documentation mismatches ... OK > * checking Rd \usage sections ... OK > * checking examples ... OK > * checking PDF version of manual ... OK > > > R CMD build longitudinalData > * checking for file 'longitudinalData/DESCRIPTION' ... OK > * preparing 'longitudinalData': > * checking DESCRIPTION meta-information ... OK > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'longitudinalData_0.5.tar.gz' > --- 8< ---------------- > > Christophe > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
>>>>> "CG" == Christophe Genolini <cgenolin at u-paris10.fr> >>>>> on Tue, 09 Jun 2009 16:17:15 +0200 writes:CG> Hi the list, I build a package. They was a mistake in CG> it, but R CMD check did not find it. Is that normal ? CG> Here is what Kurt gets (which is right, I did this CG> mistake): CG> --- 8< ---------------- CG> * checking for code/documentation mismatches ... WARNING CG> S4 class codoc mismatches from documentation object 'LongData-class': CG> Slots for class 'LongData' CG> Code: id other time traj varName CG> Docs: id time traj varName CG> --- 8< ---------------- Others have already hinted at the solution: The problem only shows in "R-devel" (2.10.x). Note that I had sent an explicit message to this list *exactly* in order to advise all package authors : Subject: [Rd] R-devel:codocClasses() now finds more --> R CMD check warnings Date: Wed, 3 Jun 2009 11:45:45 +0200 i.e. only 6 days before you saw the problem.... .... yes, I am sometimes too optimistic, assuming that people actually read what I write .... Regards anyway! Martin -- Martin Maechler, ETH Zurich