[Rd] 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: -> .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 texthtmllatex contrasts texthtmllatex example cvl texthtmllatex example nki70 texthtmllatex penalized texthtmllatex example penfittexthtmllatex plotpath texthtmllatex 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: -> .build_Rd_xref_db -> Rd_db Execution halted * checking for missing documentation entries ... OK * checking for code/
Re: [Rd] Puzzling message: "no man files in this package"
Dear Katherine,
To complicate things: whereas I was able to reproduce the problem many
times yesterday, also after restarting my computer several times and
with R 2.5.1, R 2.6.0 and R 2.6.1, the package builds and checks
_completely without errors or warnings_ and installs without the strange
message today. And I did not change _a single thing_ to the package in
between. It's a bit of a bewildering experience :-{ but at least it
solves my immediate problem :-).
I've uploaded the package to CRAN incoming (penalized_0.9-17.tar.gz),
should you still want to have a look.
My apologies for bothering you with a semi-reproducible (?!) problem.
Jelle
> -Original Message-
> From: Katharine Mullen [mailto:[EMAIL PROTECTED]
> Sent: zaterdag 1 december 2007 14:11
> To: Goeman, J.J. (MSTAT)
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Puzzling message: "no man files in this package"
>
> 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: -> .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 texthtmllatex
> > contrasts texthtmllatex example
> > cvl texthtmllatex example
> > nki70 texthtmllatex
> > penalized texthtmllatex example
> > penfittexthtmllatex
> > plotpath texthtmllatex example
> > adding MD5 sums
> >
> > * DONE (penalized)
> >
> >
> >
> > *** Rcmd check:
> >
> >
> > * using
