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...tools/libs make[6]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src' make[5]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src' make[4]: Leaving directory `/data/prog/R-2.9.1/src/library/tools' Error in namespaceExport(ns, exports) :   exportations non définies : checkDocFiles, checkDocStyle, checkFF, checkReplaceFuns, checkS3methods, checkTnF, codoc, codocClasses, codocData, undoc Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: les méthodes S3 ‘print.checkDocFiles’, ‘print.checkDocStyle’, ‘print.checkF...

...Line from manual pages in .Rd files: \method{@}{newclass}(object, name) <- value Throws this error during R CMD check ?as-cran Bad \usage lines found in documentation object ?code?: <unescaped bksl>method{@}{newclass}(object, name) <- value This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3. This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ?@? by adding ?\\@? to regexp. Please note that this now is not dependant on using or not using roxygen2 KK. > On Apr 29, 20...

...n .Rd files: > \method{@}{newclass}(object, name) <- value > Throws this error during R CMD check ?as-cran > Bad \usage lines found in documentation object ?code?: > <unescaped bksl>method{@}{newclass}(object, name) <- value > This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3. > This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ?@? by adding ?\\@? to regexp. > Please note that this now is not dependant on using or not using roxygen2 > KK. &gt...

...d{@}{newclass}(object, name) <- value > >> Throws this error during R CMD check ?as-cran > >> Bad \usage lines found in documentation object ?code?: >> <unescaped bksl>method{@}{newclass}(object, name) <- value > >> This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3. >> This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ?@? by adding ?\\@? to regexp. > >> Please note that this now is not dependant on using or not using roxygen2...

...<- value >> >>> Throws this error during R CMD check ?as-cran >> >>> Bad \usage lines found in documentation object ?code?: >>> <unescaped bksl>method{@}{newclass}(object, name) <- value >> >>> This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3. >>> This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ?@? by adding ?\\@? to regexp. >> >>> Please note that this now is not dependant on using or not usi...

...;> >>>> Throws this error during R CMD check ?as-cran >>> >>>> Bad \usage lines found in documentation object ?code?: >>>> <unescaped bksl>method{@}{newclass}(object, name) <- value >>> >>>> This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3. >>>> This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ?@? by adding ?\\@? to regexp. >>> >>>> Please note that this now is not dependant on usin...

...d.Rcheck/penalized' does not contain Rd sources Execution halted Error in tools::codocClasses(package = "penalized") : directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain Rd sources Execution halted * checking Rd \usage sections ... WARNING Error in tools::checkDocFiles(package = "penalized") : directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain Rd sources Execution halted Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to synt...

Thank you for such a quick reply, Gabriel, I am not too familiar with the package tools, so cannot speak too confidently, but below is how I see the issue currently. The issue is not for external packages to rely on unexported functions from tools::, rather the issue is that 'R CMD check ?as-cran' runs those functions from tools:: in order to check the validity of Rd files (from any

...vectors of length one. o Changes in package 'tools': - Utilities for testing and listing files, manipulating file paths, and delimited pattern matching are now exported. - Functions checkAssignFuns(), checkDocArgs() and checkMethods() have been renamed to checkReplaceFuns(), checkDocFiles(), and checkS3methods, to given better descriptions of what they do. - R itself is now used for analyzing the markup in the \usage sections. Hence in particular, replacement functions or S3 replacement methods are no longer ignored. - checkDocFiles() now also determines 'over-do...

...vectors of length one. o Changes in package 'tools': - Utilities for testing and listing files, manipulating file paths, and delimited pattern matching are now exported. - Functions checkAssignFuns(), checkDocArgs() and checkMethods() have been renamed to checkReplaceFuns(), checkDocFiles(), and checkS3methods, to given better descriptions of what they do. - R itself is now used for analyzing the markup in the \usage sections. Hence in particular, replacement functions or S3 replacement methods are no longer ignored. - checkDocFiles() now also determines 'over-do...

...and rbind() --- currently only after an explicit activation call, see ?cbind2. o New functions cdplot() and spineplot() for conditional density plots and spine plots or spinograms. Spine plots are now used instead of bar plots for x-y scatterplots where y is a factor. o checkDocFiles() in package 'tools' now checks for bad \usage lines (syntactically invalid R code). o The nonparametric variants of cor.test() now behave better in the presence of ties. The "spearman" method uses the asymptotic approximation in that case, and the "kendall"...

...and rbind() --- currently only after an explicit activation call, see ?cbind2. o New functions cdplot() and spineplot() for conditional density plots and spine plots or spinograms. Spine plots are now used instead of bar plots for x-y scatterplots where y is a factor. o checkDocFiles() in package 'tools' now checks for bad \usage lines (syntactically invalid R code). o The nonparametric variants of cor.test() now behave better in the presence of ties. The "spearman" method uses the asymptotic approximation in that case, and the "kendall"...

...ng documented in 'Writing R Extensions' ?1.3.1. The check for a missing \description has been moved from tools::checkRd() to tools::checkRdContents(). * R CMD check now visits inst/NEWS.Rd and OS-specific man subdirectories when checking Rd files. * tools::checkDocFiles() and tools::checkRdContents() now also check internal Rd files by default, but "specially" (ignoring missing documentation of arguments). * R CMD Rdiff gets option --useEx. * R CMD check now warns on non-portable uses of Fortran KIND such as INTEGER(KIND=4)...

...ng documented in 'Writing R Extensions' ?1.3.1. The check for a missing \description has been moved from tools::checkRd() to tools::checkRdContents(). * R CMD check now visits inst/NEWS.Rd and OS-specific man subdirectories when checking Rd files. * tools::checkDocFiles() and tools::checkRdContents() now also check internal Rd files by default, but "specially" (ignoring missing documentation of arguments). * R CMD Rdiff gets option --useEx. * R CMD check now warns on non-portable uses of Fortran KIND such as INTEGER(KIND=4)...