From J.J.Goeman at lumc.nl  Sat Dec  1 17:32:04 2007
From: J.J.Goeman at lumc.nl (J.J.Goeman at lumc.nl)
Date: Sat, 1 Dec 2007 17:32:04 +0100
Subject: [Rd] Puzzling message: "no man files in this package"
In-Reply-To: <Pine.GSO.4.56.0712011404170.28061@laurel.few.vu.nl>
References: <68735E80D5EB7C4F8477BF00C450D38E02F25507@mailc.lumcnet.prod.intern>
	<Pine.GSO.4.56.0712011404170.28061@laurel.few.vu.nl>
Message-ID: <68735E80D5EB7C4F8477BF00C450D38E02F25515@mailc.lumcnet.prod.intern>

 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:kate at few.vu.nl] 
> Sent: zaterdag 1 december 2007 14:11
> To: Goeman, J.J. (MSTAT)
> Cc: r-devel at 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 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
> >
> 



[Rd] Puzzling message: "no man files in this package"
J.J.Goeman at lumc.nl