replace use of CLOENV

[bbolker]

Writing R Extensions now says

@itemx CLOENV
Use @code{R_ClosureBody}, @code{R_ClosureFormals}, and
@code{R_ClosureEnv}; these were added in @R{} 4.5.0.

Rcpp uses CLOENV here

A NOTE recently appeared in lme4's CRAN checks (haven't done the archaeology yet to see exactly when this was added ...)

[eddelbuettel]

Noted, and "interesting". You are hitting that from lme4 ?

FWIW I just got going on another PR replacing the remaining DATAPTR with the DATAPTR_RO variant. This can be examined right after (but sadly reverse-depends time is counted in days given the old machine I run them on).

[eddelbuettel]

A little irritating, by the way, that a current R-devel does not report this. Is ther yet another environment variable we need to set to opt in?

[bbolker]

FWIW, running R CMD check --as-cran with the latest lme4 and the latest R-devel ("R Under development (unstable) (2025-03-08 r87909)") I do indeed get:

* checking compiled code ... NOTE
File ‘lme4/libs/lme4.so’:
  Found non-API call to R: ‘CLOENV’

Compiled code should not call non-API entry points in R.

[eddelbuettel]

I actually just rebuilt, and do not. See r87909, and "using option '--as-cran'" below. Puzzling. 1.0.14.4 is tarball I made for yesterday's PR and its rev.dep checking, it uses CLOENV unconditionally just as the repo here does.

The wrapper script kisy calls RD CMD check --output=/tmp/r --as-cran "$@". Maybe it is my ~/.R/check.Renviron-devel? Do you have one? Special values?

Never mind. You are reporting it for lme4, of course, which calls the function. Rcpp just supplies it. Try this diff if you want:

modified   inst/include/Rcpp/Function.h
@@ -99,7 +99,11 @@ namespace Rcpp{
             if( TYPEOF(fun) != CLOSXP ) {
                 throw not_a_closure(Rf_type2char(TYPEOF(fun)));
             }
-            return CLOENV(fun) ;
+            #if (defined(R_VERSION) && R_VERSION >= R_Version(4,5,0))
+            return R_ClosureEnv(fun);
+            #else
+            return CLOENV(fun);
+            #endif
         }
 
         /**

edd@rob:~/git/rcpp(feature/replace_cloenv)$ rdcc.sh Rcpp_1.0.14.4.tar.gz 
* using log directory ‘/tmp/r/Rcpp.Rcheck’
* using R Under development (unstable) (2025-03-08 r87909)
* using platform: x86_64-pc-linux-gnu                                                                    
* R was compiled by                                                                                      
    gcc (Ubuntu 14.2.0-4ubuntu2) 14.2.0
    GNU Fortran (Ubuntu 14.2.0-4ubuntu2) 14.2.0
* running under: Ubuntu 24.10   
* using session charset: UTF-8       
* using option ‘--as-cran’                         
* checking for file ‘Rcpp/DESCRIPTION’ ... OK      
* this is package ‘Rcpp’ version ‘1.0.14.4’
* package encoding: UTF-8    
* 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 ... OK
* checking for portable file names ... OK                                                                
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK                                                                 
* checking whether package ‘Rcpp’ can be installed ... [12s/11s] OK
* used C++ compiler: ‘g++-14 (Ubuntu 14.2.0-4ubuntu2) 14.2.0’
* checking installed package size ... INFO
  installed size is  9.8Mb     
  sub-directories of 1Mb or more:                                                                        
    doc       1.1Mb                              
    include   6.3Mb                   
* checking package directory ... OK
* checking for future file timestamps ... OK                                                             
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK                                                                    
* checking index information ... OK
* checking package subdirectories ... OK                                                                 
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
* checking R code for possible problems ... [8s/8s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 shell scripts ... 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’ [183s/159s]
 [183s/159s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s/14s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 NOTE
See
  ‘/tmp/r/Rcpp.Rcheck/00check.log’
for details.

edd@rob:~/git/rcpp(feature/replace_cloenv)$ 
</details>

[bbolker]

I can test if you'd like, but this seems pretty straightforward - I'm happy just knowing that a simple fix is (at least in a conceptual sense) in the upstream pipeline so that I can pass that on to CRAN if it's unresolved when I next submit a new lme4 version (and/or if they notice and hassle me about it).

[eddelbuettel]

Yes it should work. And it will be part of the next Rcpp due July.