[R-pkg-devel] Acknowledging small functions from another package
Hi, One of my packages copy-pasted some small functions (stuff like `%||%` for is.null) from ggplot2. (Both packages are MIT-licensed.) What is an appropriate way to acknowledge this in the DESCRIPTION Author: or Authors@R section? (Note that the list of ggplot2 authors is long and changing.) Cheers, David [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Acknowledging small functions from another package
On Thu, 4 May 2023 09:21:17 +0100
David Hugh-Jones wrote:
> One of my packages copy-pasted some small functions (stuff like
> `%||%` for is.null) from ggplot2. (Both packages are MIT-licensed.)
>
> What is an appropriate way to acknowledge this in the DESCRIPTION
> Author: or Authors@R section?
One way would be to mention Hadley Wickham:
https://github.com/tidyverse/ggplot2/commit/ef2f944863a0db8841bf628e9eb4a9faef5049e6#diff-8f53135445ab98749043fa52e438346bb9acae8e0185aa95f186d0aa021bb7e0
(`git blame` will also tell you that he later moved this function to a
different file).
I think that person('ggplot2 authors', role = 'cph', comment = 'The
%||% operator') is also fine, just like e.g. unitizer package mentions
the code taken from R itself.
You can also find this operator in multiple base R packages, currently
unexported (maybe some day...). They mention in the comments that the
operator is adapted from ggplot2.
--
Best regards,
Ivan
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Re: [R-pkg-devel] Acknowledging small functions from another package
On 04/05/2023 4:53 a.m., Ivan Krylov wrote:
On Thu, 4 May 2023 09:21:17 +0100
David Hugh-Jones wrote:
One of my packages copy-pasted some small functions (stuff like
`%||%` for is.null) from ggplot2. (Both packages are MIT-licensed.)
What is an appropriate way to acknowledge this in the DESCRIPTION
Author: or Authors@R section?
One way would be to mention Hadley Wickham:
https://github.com/tidyverse/ggplot2/commit/ef2f944863a0db8841bf628e9eb4a9faef5049e6#diff-8f53135445ab98749043fa52e438346bb9acae8e0185aa95f186d0aa021bb7e0
(`git blame` will also tell you that he later moved this function to a
different file).
I think that person('ggplot2 authors', role = 'cph', comment = 'The
%||% operator') is also fine, just like e.g. unitizer package mentions
the code taken from R itself.
You can also find this operator in multiple base R packages, currently
unexported (maybe some day...). They mention in the comments that the
operator is adapted from ggplot2.
I'd probably use role = "ctb" instead for "ggplot2 authors", and include
Posit PBC as a copyright holder (as ggplot2 does). Presumably you or
others are also copyright holders for your package and should also have
role = "cph" added so it doesn't give the impression that Posit owns
everything.
Duncan Murdoch
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
On 03.05.2023 23:00, Simon Urbanek wrote:
On May 4, 2023, at 3:36 AM, Martin Morgan wrote:
CRAN is fine with Bioconductor Depends: and Imports: dependencies, as
previously mentioned. This is because the CRAN maintainers explicitly configure
their system to know about Bioconductor package repositories.
That is not exactly true (at least not for all maintainers ;)). Bioconductor
packages are installed on as-needed (best-effort) basis and it is a manual
process.
Apparently for MacOS.
On Fedora/Debian/WIndows we auto install from BioC. (actually, on
Windows all BioC software packages are preinstalled).
Best,
Uwe Ligges
Ideally, Bioconductor packages would be in Suggests, because if they are not,
the package binary will be effectively broken for most users as they cannot
install it without additional steps (and no stable state can be guaranteed,
either). That's why I believe someone was suggesting a pre-flight check that
alerts the user to such situation and prints instructions to remedy it (e.g.,
to use setRepositories()) as the majority of users will have no idea what's
going on.
Cheers,
Simon
Users face a different challenge -- many users will not have identified (e.g.,
via `setRepositories()` a Bioconductor repository, so when they try to install
your package it will fail in a way that you have no control over -- a generic
message saying that the Bioconductor dependencies was not found.
You could mitigate this by advertising that your CRAN package should be installed via
`BiocManager::install("")`, which defines appropriate
repositories for both CRAN and Bioconductor, but there is no way to unambiguously communicate
this to users.
Martin
From: R-package-devel on behalf of Ruff,
Sergej
Date: Wednesday, May 3, 2023 at 11:13 AM
To: Dirk Eddelbuettel
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
Thank you, Dirk.
I see your dependencies are Suggested. I know that Suggested dependencies
should be conditional.
Do you know if Non-Cran (Bioconductor) packages need to be conditional? Do you
have any experiece regarding Non-CRAN Dependencies
and how to handle them?
I believe Duncan Murdoch's experience and opinion regarding that topic, but i
take any second and third opinion to be sure.
Thank you for your help.
Sergej
Von: Dirk Eddelbuettel
Gesendet: Mittwoch, 3. Mai 2023 16:22:09
An: Ruff, Sergej
Cc: Duncan Murdoch; Ivan Krylov; r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
Sergej,
Please consider:
- there are nearly 20k CRAN packages
- all of them are mirrored at https://github.com/cran so you can browse
- pick any one 'heavy' package you like, Seurat is a good example; there
are other examples in geospatial or bioinformatics etc
- you can browse _and search_ these to your hearts content
Here is an example of mine. In RcppArmadillo, years ago we (thanks to fine
Google Summer of Code work by Binxiang Ni) added extended support for sparse
matrices pass-through / conversione from R to C++ / Armadillo and back. That
is clearly an optional feature as most uses of (Rcpp)Armadillo use dense
matrices. So all code and test code is _conditional_. File DESCRIPTION has
Suggests: [...], Matrix (>= 1.3.0), [...], reticulate, slam
mostly for tests. I.e. We have very little R code: in one single file
R/SciPy2R.R we switched to doing this via reticulate and opee the function
with
if (!requireNamespace("reticulate", quietly=TRUE)) {
stop("You must install the 'reticulate' package (and have SciPy).",
call.=FALSE)
}
after an actual deprecation warning (as there was scipy converter once).
Similarly, the testsuites in inst/tinytests/* have several
if (!requireNamespace("Matrix", quietly=TRUE)) exit_file("No Matrix
package")
as well as
if (!requireNamespace("reticulate", quietly=TRUE)) exit_file("Package reticulate
missing")
if (!packageVersion("reticulate") >= package_version("1.14"))
exit_file("SciPy not needed on newer reticulate")
and tests for slam (another sparse matrix package besides the functionality
in Matrix).
Hopefully this brief snapshot gives you an idea. There are (likely!!)
thousandss of examples you can browse, and I am sure you will find something.
If you have further (concrete) questions please do not hesitate to use the
resource of this list.
Cheers (or I should say "mit Braunschweiger Gruessen nach Hannover),
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Re: [R-pkg-devel] Acknowledging small functions from another package
Thank you both. This sounds sensible. Yeah, add my vote for `base::%||%`!!
David
On Thu, 4 May 2023 at 10:00, Duncan Murdoch
wrote:
> On 04/05/2023 4:53 a.m., Ivan Krylov wrote:
> > On Thu, 4 May 2023 09:21:17 +0100
> > David Hugh-Jones wrote:
> >
> >> One of my packages copy-pasted some small functions (stuff like
> >> `%||%` for is.null) from ggplot2. (Both packages are MIT-licensed.)
> >>
> >> What is an appropriate way to acknowledge this in the DESCRIPTION
> >> Author: or Authors@R section?
> >
> > One way would be to mention Hadley Wickham:
> >
> https://github.com/tidyverse/ggplot2/commit/ef2f944863a0db8841bf628e9eb4a9faef5049e6#diff-8f53135445ab98749043fa52e438346bb9acae8e0185aa95f186d0aa021bb7e0
> > (`git blame` will also tell you that he later moved this function to a
> > different file).
> >
> > I think that person('ggplot2 authors', role = 'cph', comment = 'The
> > %||% operator') is also fine, just like e.g. unitizer package mentions
> > the code taken from R itself.
> >
> > You can also find this operator in multiple base R packages, currently
> > unexported (maybe some day...). They mention in the comments that the
> > operator is adapted from ggplot2.
>
> I'd probably use role = "ctb" instead for "ggplot2 authors", and include
> Posit PBC as a copyright holder (as ggplot2 does). Presumably you or
> others are also copyright holders for your package and should also have
> role = "cph" added so it doesn't give the impression that Posit owns
> everything.
>
> Duncan Murdoch
>
>
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Re: [R-pkg-devel] Acknowledging small functions from another package
IMO those functions are so small that you don't need to call them out in your DESCRIPTION. Just note in a nearby comment where they came from. Hadley On Thu, May 4, 2023 at 3:21 AM David Hugh-Jones wrote: > > Hi, > > One of my packages copy-pasted some small functions (stuff like `%||%` for > is.null) from ggplot2. (Both packages are MIT-licensed.) > > What is an appropriate way to acknowledge this in the DESCRIPTION Author: > or Authors@R section? (Note that the list of ggplot2 authors is long and > changing.) > > Cheers, > David > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- http://hadley.nz __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Acknowledging small functions from another package
In fact Martin Maechler added this in 2021:
https://github.com/wch/r-source/blob/trunk/src/library/utils/R/str.R#L19-L21
## A pearl from ggplot2 et al. NB: often needs '(.)' :%||% (
)
## *not exported* [should rather be in 'base' than exported here]
`%||%` <- function(L,R) if(is.null(L)) R else L
On 2023-05-04 5:59 a.m., David Hugh-Jones wrote:
Thank you both. This sounds sensible. Yeah, add my vote for `base::%||%`!!
David
On Thu, 4 May 2023 at 10:00, Duncan Murdoch
wrote:
On 04/05/2023 4:53 a.m., Ivan Krylov wrote:
On Thu, 4 May 2023 09:21:17 +0100
David Hugh-Jones wrote:
One of my packages copy-pasted some small functions (stuff like
`%||%` for is.null) from ggplot2. (Both packages are MIT-licensed.)
What is an appropriate way to acknowledge this in the DESCRIPTION
Author: or Authors@R section?
One way would be to mention Hadley Wickham:
https://github.com/tidyverse/ggplot2/commit/ef2f944863a0db8841bf628e9eb4a9faef5049e6#diff-8f53135445ab98749043fa52e438346bb9acae8e0185aa95f186d0aa021bb7e0
(`git blame` will also tell you that he later moved this function to a
different file).
I think that person('ggplot2 authors', role = 'cph', comment = 'The
%||% operator') is also fine, just like e.g. unitizer package mentions
the code taken from R itself.
You can also find this operator in multiple base R packages, currently
unexported (maybe some day...). They mention in the comments that the
operator is adapted from ggplot2.
I'd probably use role = "ctb" instead for "ggplot2 authors", and include
Posit PBC as a copyright holder (as ggplot2 does). Presumably you or
others are also copyright holders for your package and should also have
role = "cph" added so it doesn't give the impression that Posit owns
everything.
Duncan Murdoch
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