[Rcpp-devel] Bug: compileAttributes incorrectly handles Rcpp::export-ed functions with multiple arguments

[Davor Cubranic]

Running compileAttributes with “verbose = TRUE” was very informative:

$ Rscript -e 'Rcpp::compileAttributes(".", TRUE)'
Exports from /Users/davor/projects/Davor/myPackage/src/rcpp_hello_world.cpp:
   List rcpp_hello_world(NumericVector foo)

Exports from /Users/davor/projects/Davor/myPackage/src/rcpp_hello_world.cpp~:
   List rcpp_hello_world()

Answer: compileAttributes interprets Emacs backup files with extension “.cpp~” as source files. (My fault for not zipping up the actual source directory but the product of "R CMD build".)

Probable source of the error is in compileAttributes (Attributes.R:355):

    cppFiles <- list.files(srcDir, pattern = glob2rx("*.c*”))

You need a better way to identify C++ sources. R-exts manual says R’s make rules use .cc and .cpp for C++. (This is supposed to be recorded in R_HOME/etcR_ARCH/Makeconf, so it could potentially be processed dynamically, although I doubt that’s really necessary.)

Davor


On Jan 17, 2014, at 4:18 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

> 
> On 17 January 2014 at 15:32, Davor Cubranic wrote:
> | On 2014-01-17, at 2:55 PM, Dirk Eddelbuettel wrote:
> | 
> | > You had two mistakes here:
> | > 
> | >  i)   after you alter an interface to be used by Rcpp Attributes, you must
> | >       re-run the compileAttributes() function to update the files.  See the
> | >       vignette for details.
> | 
> | What do you mean by this? Like I said, I changed the .cpp file and re-run
> |  compileAttributes. What I uploaded is the result afterwards.
> 
> The equivalent of 
> 
>    $ cd myPackage; R -e 'Rcpp::compileAttributes(".")'
> 
> For once, I launched R and typed it by hand.
> 
> | >       (And if you use RStudio, this is done automagically)
> | 
> | So it is by devtools, on one of the functions I regularly use in my workflow, perhaps "test". If it wasn't, it would be such a pain.
> | 
> | >  ii)  Your C++ function did not work as the 'List z = ...' parameter
> | >       shadowed an already declared parameter from the function interface.
> | >       Renaming to zz or z2 works, of course.
> | 
> | I fixed it and rerun compileAttributes. Still the same problem. New version of the package is attached.
> 
> See here, based on your previous file.
> 
> edd at max:/tmp/davor/myPackage$ cat src/rcpp_hello_world.cpp 
> 
> #include <Rcpp.h>
> using namespace Rcpp;
> 
> // [[Rcpp::export]]
> List rcpp_hello_world(NumericVector z) {
> 
>    CharacterVector x = CharacterVector::create( "foo", "bar" )  ;
>    NumericVector y   = NumericVector::create( 0.0, 1.0 ) ;
>    List z2           = List::create( x, y ) ;
> 
>    return z2 ;
> }
> edd at max:/tmp/davor/myPackage$ R CMD check .
> * using log directory ‘/tmp/davor/myPackage/..Rcheck’
> * using R version 3.0.2 (2013-09-25)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘./DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘myPackage’ 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 for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>  ..Rcheck
> These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘myPackage’ can be installed ... WARNING
> Found the following significant warnings:
>  Warning: /tmp/davor/myPackage/man/myPackage-package.Rd:31: All text must be in a section
>  Warning: /tmp/davor/myPackage/man/myPackage-package.Rd:32: All text must be in a section
> See ‘/tmp/davor/myPackage/..Rcheck/00install.out’ for details.
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking DESCRIPTION meta-information ... WARNING
> Non-standard license specification:
>  What Licence is it under ?
> Standardizable: FALSE
> * checking top-level files ... OK
> * checking for left-over files ... OK
> * checking index information ... OK
> * checking package subdirectories ... WARNING
> Found the following directory with the name of a check directory:
>  ./..Rcheck
> Most likely, these were included erroneously.
> * 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 loading without being on the library search path ... OK
> * checking 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 ... WARNING
> prepare_Rd: myPackage-package.Rd:31: All text must be in a section
> prepare_Rd: myPackage-package.Rd:32: All text must be in a section
> prepare_Rd: myPackage-package.Rd:38-40: Dropping empty section \examples
> * checking Rd metadata ... OK
> * checking Rd cross-references ... WARNING
> Unknown package ‘<pkg>’ in Rd xrefs
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... WARNING
> Codoc mismatches from documentation object 'rcpp_hello_world':
> rcpp_hello_world
>  Code: function(z)
>  Docs: function()
>  Argument names in code not in docs:
>    z
> 
> * 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 compilation flags in Makevars ... OK
> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
> * checking compiled code ... OK
> * checking examples ... OK
> * checking PDF version of manual ... OK
> 
> WARNING: There were 6 warnings.
> NOTE: There was 1 note.
> See
>  ‘/tmp/davor/myPackage/..Rcheck/00check.log’
> for details.
> 
> edd at max:/tmp/davor/myPackage$ 
> 
> 
> Hope this help,  Dirk
> 
> -- 
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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