From kate at few.vu.nl  Sat Dec  1 18:18:21 2007
From: kate at few.vu.nl (Katharine Mullen)
Date: Sat, 1 Dec 2007 18:18:21 +0100 (CET)
Subject: [Rd] Puzzling message: "no man files in this package"
In-Reply-To: <68735E80D5EB7C4F8477BF00C450D38E02F25515@mailc.lumcnet.prod.intern>
References: <68735E80D5EB7C4F8477BF00C450D38E02F25507@mailc.lumcnet.prod.intern>
	<Pine.GSO.4.56.0712011404170.28061@laurel.few.vu.nl>
	<68735E80D5EB7C4F8477BF00C450D38E02F25515@mailc.lumcnet.prod.intern>
Message-ID: <Pine.GSO.4.56.0712011806520.812@laurel.few.vu.nl>

strange - but at least the strangeness resolved itself.  If the problem
was with your code as opposed to your build environment, I guess you'll
soon here from a CRAN maintainer about it (and by the way: CRAN incoming
does not allow read permission for others, so if you upload there it's
not really publicly available yet).

On Sat, 1 Dec 2007 J.J.Goeman at lumc.nl wrote:

>  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"
Katharine Mullen