R devel - Nov 2007 - Puzzling message: "no man files in this package"

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

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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>