[R-pkg-devel] Help for understanding CRAN rejection

Tue, Jul 9, 2024 3:45 AM #

(I am adding the mailing list back in Cc: because package licensing is
a complicated topic.)

? Tue, 9 Jul 2024 09:25:14 +0000
Matei Teleman <matei.teleman at unil.ch> ?????:

It looks like a link should be fine. Here are a few examples of CRAN
packages that have a non-CRAN/Bioconductor package in Suggests: without
setting up Additional_repositories:

https://CRAN.R-project.org/package=babelmixr2
https://CRAN.R-project.org/package=bandsfdp
https://cran.r-project.org/package=GCD

I'm sorry that I didn't note any of the following in my initial reply,
but what worries me about CC BY-NC-ND specifically is that out of 117
CRAN packages with a Creative Commons license and 18 of those that use
the non-FOSS "NonCommercial" clause, none use the "NoDerivatives"
clause. Your users would probably appreciate being able to install
binary builds of your package from CRAN. Does `R CMD INSTALL --build`
count as creating a derivative work, or is it "merely changing the
format"? Then again, CC BY-NC-ND _is_ mentioned in the list of CRAN
licenses, so it could work.

I found a rejected copy of your package in the archive subdirectory on
the CRAN FTP server and a GitHub repository [*] that seems to be
slightly outdated compared to the archived package. (It's best to link
to up-to-date package sources when seeking help with code.) I'm getting
an additional NOTE:

Is there a way to make some of the currently required dependencies into
conditional dependencies? R CMD check --as-cran sets the limit to 20,
so moving just one package from Imports to Suggests will silence this
particular NOTE.

I see that most of your package size comes from the data subdirectory.
CRAN policy says: "Packages should be of the minimum necessary size.
<...> Neither data nor documentation should exceed 5MB. <...> Where a
large amount of data is required (even after compression),
consideration should be given to a separate data-only package which can
be updated only rarely (since older versions of packages are archived
in perpetuity)."
Is there a way to reduce the size of the data? It's ideal if there's
only enough data to demonstrate how an algorithm works in the
\examples{} section of your documentation and to exercise as much of
your code as feasible in your tests.

Finally, were there any recommendations in the rejection e-mail from
CRAN? Sometimes NOTEs are unavoidable, but we should strive to minimise
them anyway.

Best regards,
Ivan

[*] https://github.com/GfellerLab/SuperCell

2 days later

Matei Teleman

Thu, Jul 11, 2024 7:50 AM #

Dear Ivan,

Thank you so much for your help.

I followed your advices and I reduced the size of the example data, move one package from Import to Suggest.

The type of the license is unfortunately not depending on me so I?ll try one last time with the CC license and the new improvements.

Thank your again for your time.

Have a nice day!

Best regards,

Matei

Le 9 juil. 2024 ? 12:45, Ivan Krylov <ikrylov at disroot.org> a ?crit :

(I am adding the mailing list back in Cc: because package licensing is
a complicated topic.)

? Tue, 9 Jul 2024 09:25:14 +0000
Matei Teleman <matei.teleman at unil.ch> ?????:

I?ve added ? ? SuperCell uses
[velocyto.R](https://github.com/velocyto-team/velocyto.R) for RNA
velocity. ? in the Description field. Is that enough or I need also
to directly give the command line to install the package from GitHub ?

It looks like a link should be fine. Here are a few examples of CRAN
packages that have a non-CRAN/Bioconductor package in Suggests: without
setting up Additional_repositories:

https://CRAN.R-project.org/package=babelmixr2
https://CRAN.R-project.org/package=bandsfdp
https://cran.r-project.org/package=GCD

I'm sorry that I didn't note any of the following in my initial reply,
but what worries me about CC BY-NC-ND specifically is that out of 117
CRAN packages with a Creative Commons license and 18 of those that use
the non-FOSS "NonCommercial" clause, none use the "NoDerivatives"
clause. Your users would probably appreciate being able to install
binary builds of your package from CRAN. Does `R CMD INSTALL --build`
count as creating a derivative work, or is it "merely changing the
format"? Then again, CC BY-NC-ND _is_ mentioned in the list of CRAN
licenses, so it could work.

I found a rejected copy of your package in the archive subdirectory on
the CRAN FTP server and a GitHub repository [*] that seems to be
slightly outdated compared to the archived package. (It's best to link
to up-to-date package sources when seeking help with code.) I'm getting
an additional NOTE:

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any
of them becoming unavailable.  Move as many as possible to Suggests
and use conditionally.

Is there a way to make some of the currently required dependencies into
conditional dependencies? R CMD check --as-cran sets the limit to 20,
so moving just one package from Imports to Suggests will silence this
particular NOTE.

I see that most of your package size comes from the data subdirectory.
CRAN policy says: "Packages should be of the minimum necessary size.
<...> Neither data nor documentation should exceed 5MB. <...> Where a
large amount of data is required (even after compression),
consideration should be given to a separate data-only package which can
be updated only rarely (since older versions of packages are archived
in perpetuity)."
Is there a way to reduce the size of the data? It's ideal if there's
only enough data to demonstrate how an algorithm works in the
\examples{} section of your documentation and to exercise as much of
your code as feasible in your tests.

Finally, were there any recommendations in the rejection e-mail from
CRAN? Sometimes NOTEs are unavoidable, but we should strive to minimise
them anyway.

-- 
Best regards,
Ivan

[*] https://github.com/GfellerLab/SuperCell