[Rcpp-devel] R CMD check error for sample package with module

[Yasir Suhail]

Resending, because it didn't get on the list the last time:

> I know there was a discussion earlier about R CMD check warnings, but I
> thought that a patch had fixed it. However, I am getting similar warnings
> and an error terminates R CMD check due to some Rd/latex issues.
>
> In R:
>> library(Rcpp)
>> Rcpp.package.skeleton("foo",module=T)
> Creating directories ...
> Creating DESCRIPTION ...
> Creating NAMESPACE ...
> Creating Read-and-delete-me ...
> Saving functions and data ...
> Making help files ...
> Done.
> Further steps are described in './foo/Read-and-delete-me'.
>
> Adding Rcpp settings
>  >> added RcppModules: yada
>  >> added Depends: Rcpp
>  >> added LinkingTo: Rcpp
>  >> added useDynLib directive to NAMESPACE
>  >> added Makevars file with Rcpp settings
>  >> added Makevars.win file with Rcpp settings
>  >> added example header file using Rcpp classes
>  >> added example src file using Rcpp classes
>  >> added example R file calling the C++ example
>  >> added Rd file for rcpp_hello_world
>  >> copied the example module
>> q()
> Save workspace image? [y/n/c]: y
>
> Then on the command prompt:
> $ R CMD check foo
> * using log directory ‘/private/tmp/foo.Rcheck’
> * using R version 2.14.0 (2011-10-31)
> * using platform: x86_64-apple-darwin11.0.0 (64-bit)
> * using session charset: UTF-8
> * checking for file ‘foo/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘foo’ version ‘1.0’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking whether package ‘foo’ can be installed ... WARNING
> Found the following significant warnings:
>   Warning: /private/tmp/foo/man/foo-package.Rd:31: All text must be in a
> section
>   Warning: /private/tmp/foo/man/foo-package.Rd:32: All text must be in a
> section
> See ‘/private/tmp/foo.Rcheck/00install.out’ for details.
> * 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 ... WARNING
> Non-standard license specification:
>   What Licence is it under ?
> Standardizable: FALSE
> * 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 whether the namespace can be loaded with stated dependencies ...
> OK
> * checking whether the namespace 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
> File ‘foo/R/zzz.R’:
>   .onLoad has wrong argument list ‘pkgname, libname’
>   .onLoad calls:
>     require("methods", character = TRUE, quietly = TRUE)
>
> Package startup functions should have two arguments with names starting
>   with ‘lib’ and ‘pkg’, respectively.
> Package startup functions should not change the search path.
> See section ‘Good practice’ in ?.onAttach.
>
> * checking Rd files ... WARNING
> prepare_Rd: foo-package.Rd:31: All text must be in a section
> prepare_Rd: foo-package.Rd:32: All text must be in a section
> prepare_Rd: foo-package.Rd:38-40: Dropping empty section \examples
> * checking Rd metadata ... OK
> * checking Rd cross-references ... WARNING
> Unknown package(s) ‘<pkg>’ in Rd xrefs
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
>   ‘World’ ‘bar’ ‘bla’ ‘bla1’ ‘bla2’ ‘hello’
> All user-level objects in a package should have documentation entries.
> See the chapter ‘Writing R documentation files’ in the ‘Writing R
> Extensions’ manual.
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... OK
> * checking line endings in C/C++/Fortran sources/headers ... OK
> * checking line endings in Makefiles ... OK
> * checking for portable compilation flags in Makevars ... OK
> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
> * checking compiled code ... OK
> * checking examples ... OK
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> LaTeX errors found:
> * checking PDF version of manual without hyperrefs or index ... ERROR