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 [EMAIL PROTECTED] 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:[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: <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@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel