From gavin.simpson at ucl.ac.uk  Sat Mar 26 22:39:37 2011
From: gavin.simpson at ucl.ac.uk (Gavin Simpson)
Date: Sat, 26 Mar 2011 21:39:37 +0000
Subject: [Rd] rebuilding vignettes in 2.13-0-alpha fails if name of source
 dir is not package name
Message-ID: <1301175577.2723.24.camel@chrysothemis.geog.ucl.ac.uk>

Dear list,

I have been checking my package ('analogue') using R2.13-0-alpha
(details of exact svn version appended below) and the R CMD check
procedure is generating an error rebuilding a vignette in the package,
which raises a NOTE in the check.

The log printed to screen during check shows:

....
* checking re-building of vignettes ... NOTE
Error in re-building vignettes:
  ...
Error in pkgVignettes(package = package, dir = dir, lib.loc = lib.loc) : 
  directory '/home/gavin/work/R/packages/analogue/analogue_check/pkg.Rcheck/vign_test/analogue' does not exist
Calls: buildVignettes -> pkgVignettes
Execution halted

* checking PDF version of manual ... OK

The entire log is appended below the sessionInfo() output.

If I look in the directory where I am checking the package, I have
pkg.Rcheck and inside the I have vign_test. Inside that directory I have
a 'pkg' directory, but no 'analogue' directory.

My source is in a directory 'pkg' after the set-up provided by
r-forge.r-project.net.

It looks like the code expects a directory with the same name as the
package name in vign_test or the directory in vign_test is not being
named correctly.

R CMD check proceeds without this issue in R 2.12-patched.

If you need further information, let me know.

All the best,

Gavin

> sessionInfo()
R version 2.13.0 alpha (2011-03-26 r55068)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base

00check.log - ignore the missing documentation and documentation
mismatch warnings - they are for code I am currently checking/working on
that only exists in my local source tree not in the R-forge repository
nor in the package sources on CRAN.

* using log directory ?/home/gavin/work/R/packages/analogue/analogue_check/pkg.Rcheck?
* using R version 2.13.0 alpha (2011-03-26 r55068)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ?pkg/DESCRIPTION? ... OK
* checking extension type ... Package
* this is package ?analogue? version ?0.7-0?
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ?analogue/src? contains object files.
* checking for executable files ... OK
* checking whether package ?analogue? can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 package can be unloaded cleanly ... 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 ... NOTE
prcurve: no visible global function definition for ?pcget.lam?
* checking Rd files ... NOTE
prepare_Rd: coreData.Rd:19-20: Dropping empty section \usage
prepare_Rd: coreData.Rd:21-22: Dropping empty section \arguments
prepare_Rd: coreData.Rd:23-24: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  OOB ageModel ageModel.coreData ageModel.default dates dates.coreData
  dates.default depths depths.coreData depths.default distance2
  distance2.default gradientDist gradientDist.cca gradientDist.default
  gradientDist.prcurve intervals intervals.coreData intervals.default
  lines.gradientDist metadata metadata.coreData plot.gradientDist
  points.gradientDist randomWA randomWA.default rbind.coreData varExpl
  varExpl.cca varExpl.default varExpl.prcurve waPred
All user-level objects in a package should have
documentation entries.
See the chapter 'Writing R documentation files' in manual
'Writing R Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'prcurve':
prcurve
  Code: function(X, method = c("ca", "pca", "random"), smoother =
                 smoothSpline, complexity, vary = FALSE, maxComp,
                 finalCV = FALSE, axis = 1, rank = FALSE, stretch = 2,
                 maxit = 10, trace = FALSE, thresh = 0.001, plotit =
                 FALSE, fitFUN = c("princurve", "pcurve"), latent =
                 FALSE, ...)
  Docs: function(X, method = c("ca", "pca", "random"), smoother =
                 smoothSpline, complexity, vary = FALSE, maxComp,
                 finalCV = FALSE, axis = 1, rank = FALSE, stretch = 2,
                 maxit = 10, trace = FALSE, thresh = 0.001, plotit =
                 FALSE, ...)
  Argument names in code not in docs:
    fitFUN latent
  Mismatches in argument names:
    Position: 15 Code: fitFUN Docs: ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ?inst/doc? ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignettes ... NOTE
Error in re-building vignettes:
  ...
Error in pkgVignettes(package = package, dir = dir, lib.loc = lib.loc) : 
  directory '/home/gavin/work/R/packages/analogue/analogue_check/pkg.Rcheck/vign_test/analogue' does not exist
Calls: buildVignettes -> pkgVignettes
Execution halted

* checking PDF version of manual ... OK
WARNING: There were 3 warnings, see
  ?/home/gavin/work/R/packages/analogue/analogue_check/pkg.Rcheck/00check.log?
for details

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%



[Rd] rebuilding vignettes in 2.13-0-alpha fails if name of source dir is not package name
Gavin Simpson