date:20250707

Re: [R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

2025-07-07 Thread Duncan Murdoch


On 2025-07-07 11:23 a.m., Jan van der Laan wrote:


I have a package, which I am thinking to submit to CRAN. It can output
graphics/plots to the kitty terminal (https://sw.kovidgoyal.net/kitty/).
However, I am not sure if and how I should indicate the dependency on
kitty. The package builds and installs fine without kitty. However, you
can't really use it without it (it will generate errors when you try).

Two possible fields in the DESCRIPTION could be:

SystemRequirements: kitty

And since, kitty only runs on macos and linux:

OS_type: unix

Should I add these? Like above?


I think the SystemRequirements field is enough.  *Your package* doesn't 
depend on unix, it just depends on kitty.


Duncan Murdoch

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Re: [R-pkg-devel] Help with CRAN Submission Feedback

2025-07-07 Thread Reed A. Cartwright

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


If this passes, I'll let you know.

Cheers,
Reed


On Mon, Jul 7, 2025 at 11:43 AM Kevin Ushey  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
>  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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[R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

2025-07-07 Thread Jan van der Laan




I have a package, which I am thinking to submit to CRAN. It can output 
graphics/plots to the kitty terminal (https://sw.kovidgoyal.net/kitty/). 
However, I am not sure if and how I should indicate the dependency on 
kitty. The package builds and installs fine without kitty. However, you 
can't really use it without it (it will generate errors when you try).


Two possible fields in the DESCRIPTION could be:

SystemRequirements: kitty

And since, kitty only runs on macos and linux:

OS_type: unix

Should I add these? Like above?

Thanks!

Jan

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Re: [R-pkg-devel] Help with CRAN Submission Feedback

2025-07-07 Thread Uwe Ligges


Please ignore that comment:
I think "tools/config/configure.R" was meant, but that seems fine, too.

Best,
Uwe Ligges

On 07.07.2025 20:42, Kevin Ushey 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
 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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Re: [R-pkg-devel] Help with CRAN Submission Feedback

2025-07-07 Thread Kevin Ushey

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
 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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Re: [R-pkg-devel] Help with CRAN Submission Feedback

2025-07-07 Thread Reed A. Cartwright

Dear Uwe,

Thank you for letting me know that I can ignore that comment.

Cheers,
Reed

On Mon, Jul 7, 2025 at 12:02 PM Uwe Ligges
 wrote:
>
> Please ignore that comment:
> I think "tools/config/configure.R" was meant, but that seems fine, too.
>
> Best,
> Uwe Ligges
>
> On 07.07.2025 20:42, Kevin Ushey 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
> >  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
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

2025-07-07 Thread Jan van der Laan


OK. Thanks!

I wasn't sure if the 'SystemRequirements' field was intended just for 
dependencies needed for building and installing the package like 
libraries or a 'non-default C++ standard'. Or that it should also be 
used for dependencies needed at run-time.


Jan


On 07-07-2025 17:53, Duncan Murdoch wrote:

On 2025-07-07 11:23 a.m., Jan van der Laan wrote:


I have a package, which I am thinking to submit to CRAN. It can output
graphics/plots to the kitty terminal (https://sw.kovidgoyal.net/kitty/).
However, I am not sure if and how I should indicate the dependency on
kitty. The package builds and installs fine without kitty. However, you
can't really use it without it (it will generate errors when you try).

Two possible fields in the DESCRIPTION could be:

SystemRequirements: kitty

And since, kitty only runs on macos and linux:

OS_type: unix

Should I add these? Like above?


I think the SystemRequirements field is enough.  *Your package* doesn't 
depend on unix, it just depends on kitty.


Duncan Murdoch



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Re: [R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

Re: [R-pkg-devel] Help with CRAN Submission Feedback

[R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

Re: [R-pkg-devel] Help with CRAN Submission Feedback

Re: [R-pkg-devel] Help with CRAN Submission Feedback

Re: [R-pkg-devel] Help with CRAN Submission Feedback

Re: [R-pkg-devel] Indicate dependency on kitty in DESCRIPTION

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