Hi Reed,

Have you received any feedback yet? My only guess is that this was a
false positive from some static analysis tools on the CRAN
maintainer's side;
https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Package-subdirectories
says that:

> Subdirectory tools is the preferred place for auxiliary files needed during 
> configuration, and also for sources need to re-create scripts (e.g. M4 files 
> for autoconf: some prefer to put those in a subdirectory m4 of tools).

Perhaps the presence of these files within a CRAN package submission
is causing something to trip up. If not, let me know if there's
anything I can change on the 'configure' side to help resolve this.

Did you also get a warning about the 'cleanup.R' file? That is, my
guess is that the presence of these two files
(https://github.com/reedacartwright/ironseed/tree/main/tools/config)
is somehow causing the issue.

Thanks,
Kevin

On Sat, Jul 5, 2025 at 2:13 PM Reed A. Cartwright
<racartwri...@gmail.com> wrote:
>
> Dear All,
>
> I submitted a new package ("ironseed") [1] to CRAN. I am not sure how
> to address one feedback message or even what is causing it. It might
> be related to Kevin Ushey's R scripts that I am using to configure the
> package during installation [2]. The message that I received is below.
>
> """
> Please ensure that your functions do not write by default or in your
> examples/vignettes/tests in the user's home filespace (including the
> package directory and getwd()). This is not allowed by CRAN policies.
> Please omit any default path in writing functions. In your
> examples/vignettes/tests you can write to tempdir().
> -> tools/config.Rtools/config/configure.R
> """
>
> `tools/config.Rtools/config/configure.R` is not a file in my package.
> So I assume that this report is saying that it is being created during
> installation, but I can't reproduce it. My package does read and
> execute `tools/config/configure.R` during installation, so right now
> my guess is that my configure script is somehow creating
> `tools/config.Rtools/config/configure.R` when I try to read
> `tools/config/configure.R`. Any help figuring this out would be
> appreciated.
>
> [1] https://github.com/reedacartwright/ironseed
> [2] https://github.com/kevinushey/configure
>
> Thanks,
> Reed
>
> --
> Reed A. Cartwright, PhD
> Associate Professor of Life Sciences
> TEACh Representative - Evolution and Computational Courses
> School of Life Sciences and The Biodesign Institute
> Arizona State University
> ==================
> Address: The Biodesign Institute, PO Box 876401, Tempe, AZ 85287-6401 USA
> Packages: The Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ
> 85287-6401 USA
> Office: Biodesign B-220C, 1-480-965-9949
> Website: http://cartwrig.ht/
>
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