Hi Kevin,

First, thanks for the configure.R package. I needed to check for the
presence of two functions during compilation and it helped simplify
the process for me.

I resubmitted to CRAN yesterday under the assumption that this report
was being generated from a static analysis. I made the following
changes to `tools/config.R`.

* Removed all the `@export` lines.
* Removed the default `path = "."` in `configure_directory()`.
* Removed the `use_configure()` function.

You can see the fill diff at
<https://github.com/reedacartwright/ironseed/compare/8522d28...45a0f23#diff-6c174165097fa11900454663ab7b0a589bb0fc8f7e41b25d8b11833674ad4d91>

If this passes, I'll let you know.

Cheers,
Reed


On Mon, Jul 7, 2025 at 11:43 AM Kevin Ushey <kevinus...@gmail.com> wrote:
>
> 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/
> >
> > ______________________________________________
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel

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