[R-pkg-devel] How to handle CRAN warning regarding stdout/stderr coming from code in upstream C library

[Balasubramanian Narasimhan]

While on the subject, one useful workflow I have adopted (e.g. package 
cubature) is to clone the underlying C library to a Github repo. (Always 
happy to hear of others!)

Then create a branch called `R_pkg` and make changes on this branch and 
use it as the source for your C library. Not only does it account for 
your changes, but also helps you keep abreast of future modifications to 
the original.

In fact, the problems you mention are exactly what I had to deal with 
recently.

-Naras

On 5/31/25 4:15 PM, SN248 wrote:
> Dear R package developers
>
> I am getting the following errors in my package (sundialr -
> https://github.com/sn248/sundialr) which is a wrapper around SUNDIALS C
> library. The warnings are as follows:
>
> ❯ checking compiled code ...
>> WARNING File ‘sundialr/libs/sundialr.so’:
>> Found ‘abort’, possibly from ‘abort’ (C) Object:
>> ‘../inst/lib/libsundials_core.a’
>> Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Object:
>> ‘../inst/lib/libsundials_core.a’
>> Found ‘stderr’, possibly from ‘stderr’ (C) Object:
>> ‘../inst/lib/libsundials_core.a’
>> Found ‘stdout’, possibly from ‘stdout’ (C) Objects:
>> ‘../inst/lib/libsundials_core.a’, ‘../inst/lib/libsundials_cvodes.a’,
>> ‘../inst/lib/libsundials_idas.a’, ‘../inst/lib/libsundials_nvecserial.a’
>> 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. See ‘Writing portable packages’ in the ‘Writing
>> R Extensions’ manual.
>
> See them at -
> https://cran-archive.r-project.org/web/checks/2025/2025-05-12_check_results_sundialr.html
>
> As far as I understand these warnings are coming from the following files:
>
> 1. 'abort' coming from -
> https://github.com/sn248/sundialr/blob/ace6865ac0bc995190bc4c354a8823ea8d3bd358/src/sundials/sundials/sundials_errors.c#L87
>
> 2. I cannot find the file/line where 'puts' is coming from
>
> 3. stderr/stdout -- too many instances in SUNDIALS C code to list here,
> e.g.,
> https://github.com/sn248/sundialr/blob/ace6865ac0bc995190bc4c354a8823ea8d3bd358/src/sundials/arkode/arkode.c#L1285
>
> In principle, I don't want to change anything in the upstream C library
> code while including it in my package. Is this any other way to resolve
> these warnings as the package has been archived because of these warnings
> now.
>
> Thanks
> Satya
>
> 	[[alternative HTML version deleted]]
>
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