[Rd] Puzzling message: "no man files in this package"

[Katharine Mullen]

Dear Jelle,

Could you put the package somewhere public?  This would make it easier to
diagnose the problem.

On Fri, 30 Nov 2007 J.J.Goeman at lumc.nl 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
>
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