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these warnings as the package has been archived because of these warnings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]]
______________________________________________
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
______________________________________________
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
