[R] Fix CRAN warnings for 19.0.1 about compiled code

[jonkeane]

Describe the enhancement requested

I received a message from CRAN that we need to fix issues they are seeing in the next two weeks.

#45870 will fix the symbols issues, which is great (and I believe we can cherrypick that easily).

There is also:

Found non-API calls to R: ‘DATAPTR’, ‘OBJECT’

(from #45850 (comment))

The non-API calls probably deserve a separate issue. They might be coming from cpp11, or there might be calls we will need to remove and use something else for them. #43044 was similar and https://cran.rstudio.com/doc/manuals/r-devel/R-exts.html#Moving-into-C-API-compliance-1 might have helpful pointers

Also related to non-API calls, there is was thread from the r-package-devel mailing list yesterday: https://stat.ethz.ch/pipermail/r-package-devel/2025q1/011543.html

I can take a look at the non-api calls (this week). @amoeba might you be up for helping cut a patch release for R only? it should only need to be R-source only changes, so we don't need a full arrow release or anything.

Component(s)

R

[amoeba]

Thanks @jonkeane. I'd be happy to create an R-only patch release for this. I'll keep an eye out for a PR for the non-api thing.

[amoeba]

I'm going to drop the current check results below in a details tag for later reference:

CRAN check warnings for 19.0.1 (as of 2025/03/26)

Check Details

Version: 19.0.1
Check: compiled code
Result: WARN 
  File ‘arrow/libs/arrow.so’:
    Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libparquet.a’
    Found ‘abort’, possibly from ‘abort’ (C)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_acero.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘stderr’, possibly from ‘stderr’ (C)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘stdout’, possibly from ‘stdout’ (C)
      Object:
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
  File ‘arrow/libs/arrow.so’:
    Found non-API calls to R: ‘DATAPTR’, ‘OBJECT’
  
  Compiled code should not call entry points which might terminate R nor
  write to stdout/stderr instead of to the console, nor use Fortran I/O
  nor system RNGs nor [v]sprintf.
  Compiled code should not call non-API entry points in R.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
  and section ‘Moving into C API compliance’ for issues with the use of
  non-API entry points.
Flavors: [r-devel-linux-x86_64-debian-clang](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/arrow-00check.html), [r-devel-linux-x86_64-debian-gcc](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/arrow-00check.html), [r-patched-linux-x86_64](https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/arrow-00check.html)

Version: 19.0.1
Check: compiled code
Result: WARN 
  File ‘arrow/libs/arrow.so’:
    Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libparquet.a’
    Found ‘abort’, possibly from ‘abort’ (C)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_acero.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘stderr’, possibly from ‘stderr’ (C)
      Objects: ‘../libarrow/arrow-19.0.1/lib/libarrow.a’,
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
    Found ‘stdout’, possibly from ‘stdout’ (C)
      Object:
        ‘../libarrow/arrow-19.0.1/lib/libarrow_bundled_dependencies.a’
  File ‘arrow/libs/arrow.so’:
    Found non-API calls to R: ‘DATAPTR’, ‘OBJECT’
  
  Compiled code should not call entry points which might terminate R nor
  write to stdout/stderr instead of to the console, nor use Fortran I/O
  nor system RNGs nor [v]sprintf.
  Compiled code should not call non-API entry points in R.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
  and section ‘Moving into C API compliance’ for issues with the use of
  non-API entry points.
Flavor: [r-devel-linux-x86_64-fedora-clang](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/arrow-00check.html)

Version: 19.0.1
Check: whether package can be installed
Result: ERROR 
  Installation failed.
Flavor: [r-devel-linux-x86_64-fedora-gcc](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/arrow-00check.html)

Version: 19.0.1
Check: compiled code
Result: WARN 
  File 'arrow/libs/x64/arrow.dll':
    Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
      Objects: '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libthrift.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64/libthrift.a'
    Found '_ZSt4cout', possibly from 'std::cout' (C++)
      Objects: '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libparquet.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64/libparquet.a'
    Found '_assert', possibly from 'assert' (C)
      Objects: '../windows/arrow-19.0.1/lib/x64/libnghttp2.a',
        '../windows/arrow-19.0.1/lib/x64/libssh2.a'
    Found '_exit', possibly from '_exit' (C)
      Objects: '../windows/arrow-19.0.1/lib/i386/libbrotlienc.a',
        '../windows/arrow-19.0.1/lib/i386/libbz2.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libcrypto.a',
        '../windows/arrow-19.0.1/lib/x64/libcrypto.a'
    Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
      Objects: '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow_acero.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libaws-c-common.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libaws-cpp-sdk-transfer.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libnghttp2.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow_acero.a',
        '../windows/arrow-19.0.1/lib/x64/libarrow_bundled_dependencies.a',
        '../windows/arrow-19.0.1/lib/x64/libaws-c-common.a',
        '../windows/arrow-19.0.1/lib/x64/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64/libaws-cpp-sdk-transfer.a',
        '../windows/arrow-19.0.1/lib/x64/libnghttp2.a'
    Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
      Objects: '../windows/arrow-19.0.1/lib/x64-ucrt/libbrotlienc.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libbz2.a',
        '../windows/arrow-19.0.1/lib/x64/libbrotlienc.a',
        '../windows/arrow-19.0.1/lib/x64/libbz2.a'
    Found 'rand', possibly from 'rand' (C)
      Objects:
        '../windows/arrow-19.0.1/lib/x64-ucrt/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64-ucrt/libthrift.a',
        '../windows/arrow-19.0.1/lib/x64/libaws-cpp-sdk-core.a',
        '../windows/arrow-19.0.1/lib/x64/libthrift.a'
  File 'arrow/libs/x64/arrow.dll':
    Found non-API calls to R: 'DATAPTR', 'OBJECT'
  
  Compiled code should not call entry points which might terminate R nor
  write to stdout/stderr instead of to the console, nor use Fortran I/O
  nor system RNGs nor [v]sprintf.
  Compiled code should not call non-API entry points in R.
  
  See 'Writing portable packages' in the 'Writing R Extensions' manual,
  and section 'Moving into C API compliance' for issues with the use of
  non-API entry points.
Flavor: [r-devel-windows-x86_64](https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/arrow-00check.html)

[jonkeane]

Issue resolved by pull request 45951
#45951