Dear Jelle, Could you put the package somewhere public? This would make it easier to diagnose the problem.
On Fri, 30 Nov 2007 [EMAIL PROTECTED] wrote: > Dear R developers, > > When building/checking my package (in R 2.6.1 under windows) I run into > some messages that I do not completely understand and that do not give > me precise enough leads to pinpoint where the error in my package is. I > would be very grateful for any suggestions. Did anyone else encounter > the same problem before? > > When building or installing the package, I get the message (no error or > warning, just a message) "no man files in this package", instead of the > usual "installing man source files". This puzzles me greatly, as I have > a "man" subdirectory with several .Rd files, all of which seem to be > properly handled later on in the install/build process, when the > "Building/Updating help files" step seems to go fine for all Rd files. > Both install and build run to conclusion without reporting formal errors > or warnings. > > Next, Rcmd check gives me a lot of nice OK's (even: * checking Rd files > ... OK), and then > > * checking Rd cross-references ... WARNING > Error in Rd_db(package, lib.loc = lib.loc) : > directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain > Rd objects > Calls: <Anonymous> -> .build_Rd_xref_db -> Rd_db > Execution halted > > Again puzzling! I get the impression that the error message is not meant > for me (I'm not the one who is supposed to put Rd objects into > M:/R/packages/penalized.Rcheck/penalized, am I?), but that the error > somehow prevents me from seeing the real warning. > > The same warning with error is repeated several times at "checking for > code/documentation mismatches" and at "checking Rd \usage sections". > > It's obvious that there is something wrong in my .Rd files. But I can't > find any mistakes by just looking through them, and the error messages > don't mean much to me. Did I overlook something obvious? > > The complete install and build output is given below. > > Thanks in advance, > > Jelle > > > > > ************************ > *** Rcmd install: > ************************ > > installing R.css in M:/R/packages/penalized.Rcheck > > > ---------- Making package penalized ------------ > adding build stamp to DESCRIPTION > installing NAMESPACE file and metadata > installing R files > installing inst files > installing data files > preparing package penalized for lazy loading > Loading required package: survival > Loading required package: splines > Creating a new generic function for "coefficients" in "penalized" > Creating a new generic function for "residuals" in "penalized" > Creating a new generic function for "fitted.values" in "penalized" > Creating a new generic function for "weights" in "penalized" > Creating a new generic function for "plot" in "penalized" > Creating a new generic function for "as.matrix" in "penalized" > Creating a new generic function for "time" in "penalized" > Creating a new generic function for "as.list" in "penalized" > no man files in this package > installing indices > not zipping data > installing help > >>> Building/Updating help pages for package 'penalized' > Formats: text html latex example chm > breslow text html latex > contrasts text html latex example > cvl text html latex example > nki70 text html latex > penalized text html latex example > penfit text html latex > plotpath text html latex example > adding MD5 sums > > * DONE (penalized) > > > ************************ > *** Rcmd check: > ************************ > > * using log directory 'M:/R/packages/penalized.Rcheck' > * using R version 2.6.1 (2007-11-26) > * checking for file 'penalized/DESCRIPTION' ... OK > * this is package 'penalized' version '0.9-17' > * checking package name space information ... OK > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking whether package 'penalized' 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 whether the name space 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 cross-references ... WARNING > Error in Rd_db(package, lib.loc = lib.loc) : > directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain > Rd objects > Calls: <Anonymous> -> .build_Rd_xref_db -> Rd_db > Execution halted > * checking for missing documentation entries ... OK > * checking for code/documentation mismatches ... WARNING > Error in tools::codoc(package = "penalized") : > directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain > Rd sources > Execution halted > Error in tools::codocData(package = "penalized") : > directory 'M:/R/packages/penalized.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 syntactically valid R code. > See the chapter 'Writing R documentation files' in manual 'Writing R > Extensions'. > Error in tools::checkDocStyle(package = "penalized") : > directory 'M:/R/packages/penalized.Rcheck/penalized' does not contain > Rd sources > Execution halted > The \usage entries for S3 methods should use the \method markup and not > their full name. > See the chapter 'Writing R documentation files' in manual 'Writing R > Extensions'. > * checking data for non-ASCII characters ... OK > * creating penalized-Ex.R ... OK > * checking examples ... OK > * checking package vignettes in 'inst/doc' ... OK > * creating penalized-manual.tex ... OK > * checking penalized-manual.tex ... OK > > > > > > www.msbi.nl/goeman > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
