[Rd] R CMD check and CRAN's Rust policy
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Mon Mar 31 19:04:30 CEST 2025
On 2025-03-31 12:41 p.m., Josiah Parry wrote:
> Duncan, the changes to symbols checking was introduced March 22nd see
> https://bugs.r-project.org/show_bug.cgi?id=18789
> <https://bugs.r-project.org/show_bug.cgi?id=18789> and
> https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/03/22#n2025-03-22 <https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/03/22#n2025-03-22>. But that is unrelated.
Sorry, I missed that.
>
> To Tim's comment—the check is a simple grep of the installation log for
> "Downloading crates." This could be easily circumvented on CRAN and
> locally by suppressing stdout/err. But that would be adversarial and I
> would like to adhere to the intent of the check.
I think Tim was suggesting that you modify your Github action to ignore
this particular warning. The warning would still appear, but it
wouldn't cause a check failure.
Duncan Murdoch
>
>
>
> On Mon, Mar 31, 2025 at 9:23 AM Duncan Murdoch <murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>> wrote:
>
> On 2025-03-31 11:50 a.m., Josiah Parry wrote:
> > Following up with this as I address the new R-devel "Compiled code
> > should not call entry points which might terminate R" WARNING and
> this
> > issue has reared its head again.
> >
> > Would a path forward be an environment variable similar
> > to _R_CHECK_CRAN_INCOMING_ to skip this check primarily for GitHub
> > Actions and CI?
>
> The "Compiled code should not call entry points which might
> terminate R"
> isn't a new warning. I think the last change to it was made in 2022.
>
> Maybe your code, or code in one of the libraries you use, has changed?
>
> Duncan Murdoch
>
>
>
>
> >
> > Or, alternatively, if this could be a NOTE when the `--as-cran` flag
> > isn't set but a WARNING when it is?
> >
> > Re-vendoring dependencies each time they are changed during the
> > development lifecycle is quite a bit. However, vendoring once
> prior to
> > publishing makes good sense.
> >
> > Is there a balance we can strike here to lower development
> friction but
> > also ensure the robust package installation requirements when
> expected?
> >
> > Using
> >
> >
> >
> >
> > On Sun, Mar 2, 2025 at 11:42 AM Duncan Murdoch
> <murdoch.duncan using gmail.com <mailto:murdoch.duncan using gmail.com>
> > <mailto:murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>>> wrote:
> >
> > On 2025-03-02 1:09 p.m., Ben Bolker wrote:
> > > I, like Duncan, am just following along here. I think there
> > might be
> > > two distinct questions which it would be useful to keep
> distinct:
> > >
> > > * how to silence the rust-check if desired?
> > >
> > > rather than debating whether the rust-check should be
> always-on,
> > > on-for-CRAN-only, etc., would it provide for useful
> flexibility
> > to add
> > > an environment variable that enables/disables this
> > functionality? There
> > > are already 168 of these environment variables, how much would
> > one more
> > > cost?
> >
> > I may have misunderstood Josiah. I thought his message said
> that it is
> > already easy to silence the check, by stopping the code from
> issuing
> > the
> > message the check is looking for.
> >
> > Presumably the package shouldn't do that, but if there's an
> environment
> > variable that can be set to do it, then the repository or
> user can
> > choose to do it, so there's no need for R to add another
> environment
> > variable.
> >
> > BTW, as far as I can see current R-devel doesn't issue an
> error, it
> > just
> > issues warnings about two issues:
> >
> > - the package is downloading crates
> > - the rustc compiler doesn't report a version number
> >
> > Duncan Murdoch
> >
> > >
> > > I'm not sure how adding an environment variable to
> allow easier
> > > user/alternate-repository control of the check is "against the
> > spirit of
> > > the check" ...
> > >
> > > All the existing check-regulating env variables ...
> > >
> > > cd src/library/tools/R
> > > grep 'Sys.getenv("_R_CHECK' * | sed -e
> 's/^.*Sys.getenv(//' | sed -e
> > > 's/[,)].*//' | sort | uniq | wc
> > >
> > >
> > > * should CRAN allow Rust crates to be downloaded?
> > >
> > > This is a much more fundamental policy decision, which
> I have no
> > > opinion about.
> > >
> > > cheers
> > > Ben Bolker
> > >
> > >
> > >
> > >
> > > On 2025-03-02 12:21 p.m., Duncan Murdoch wrote:
> > >> On 2025-03-02 11:03 a.m., Josiah Parry wrote:
> > >>> Well this has surely veered off course!
> > >>>
> > >>> As the one who filed the BugZilla report, I'd like to
> redirect the
> > >>> conversation and provide further context.
> > >>>
> > >>> The question should be /"how do we get a dialogue
> started on this
> > >>> bugzilla issue before the next minor /
> > >>> /release of R?"/
> > >>
> > >> Isn't this exactly that dialogue?
> > >>
> > >>>
> > >>> The current check for Rust-based R package's downloading
> external
> > >>> dependencies works by looking at
> > >>> the output logs for the presence of "Downloading
> crates." This
> > can is
> > >>> an entirely fine requirement for
> > >>> CRAN—however, due to the fact that it is an error, packages
> > >>> distributed through other repositories
> > >>> fail the R-CMD check.
> > >>
> > >> I think you misunderstood me. CRAN shares the view I
> gave that you
> > >> should be able to run old code to reproduce old results, but
> > they aren't
> > >> the only ones. That's always been a goal of R.
> > >>
> > >>> Folks who use R-universe or PPM or some mysterious third
> thing
> > may not
> > >>> share the same philosophy as
> > >>> CRAN and prefer the convenience of fetching the
> dependencies at
> > >>> compile time and not vendoring them.
> > >>> An alternative would be for the check to be optionally
> skipped or
> > >>> become a NOTE when the CRAN
> > >>> flag is not set and an ERROR otherwise. Skipping this CRAN
> > check is as
> > >>> easy as adding `--quiet`
> > >>> or setting an environment variable—but that is against the
> > spirit of
> > >>> the check.
> > >>
> > >> If it is that easy to skip the check, then I really don't see
> > the issue.
> > >> Just ask the repository where you want to put your
> package to
> > put that
> > >> option or environment variable in place, and there's no
> longer a
> > problem.
> > >>
> > >> Duncan Murdoch
> > >>
> > >>> Ideally, the check can remain, but scoped appropriately.
> > >>>
> > >>>
> > >>> On Sun, Mar 2, 2025 at 6:49 AM Duncan Murdoch
> > >>> <murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com> <mailto:murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>>
> > <mailto:murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com> <mailto:murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>>>>
> > wrote:
> > >>>
> > >>> You seem to be taking a confontational tone, which
> isn't
> > likely to
> > >>> encourage a reasonable dialogue.
> > >>>
> > >>> I've looked for other messages on this, and didn't
> see any
> > besides
> > >>> this
> > >>> one explaining why including check_rust() in the
> checks is
> > a problem.
> > >>> The problem you talk about here is that it encourages
> > vendoring,
> > >>> which
> > >>> makes it harder for package authors to count downloads.
> > >>>
> > >>> To be honest, that doesn't seem like a very serious
> > problem. I
> > >>> assume
> > >>> the packages ("crates") we are talking about are open
> > source, so
> > >>> this is
> > >>> entirely in the spirit of how they are allowed to be
> > distributed.
> > >>>
> > >>> If they aren't open source, then users of those
> packages
> > should be
> > >>> warned about that, and a check failure is a good
> way to do
> > that.
> > >>>
> > >>> So you need to explain why it is important to be
> able to
> > download and
> > >>> install software and not be warned about it.
> > >>>
> > >>> I am not in R Core or CRAN, but I can suggest why it is
> > better to
> > >>> include source in the package: it makes the use of
> that
> > package more
> > >>> reliable in the future. It's not uncommon to run an R
> > computation
> > >>> that
> > >>> was written a few years ago. Sometimes libraries or R
> > have changed,
> > >>> and
> > >>> a user will need to go back to a previous version to
> > reproduce the
> > >>> calculation. Being able to able to rebuild a
> system as it
> > would have
> > >>> been back then is important.
> > >>>
> > >>> Is that possible if the package needs to make a
> download? The
> > >>> download
> > >>> site that worked a few years ago may no longer
> exist. If
> > the site
> > >>> exists, the code versions there may be different.
> > >>>
> > >>> Those are some of the issues that Simon was
> alluding to.
> > >>>
> > >>> Duncan Murdoch
> > >>>
> > >>>
> > >>>
> > >>> On 2025-03-02 5:45 a.m., Mossa Merhi Reimert via
> R-devel
> > wrote:
> > >>> > Dear Simon Urbanek,
> > >>> >
> > >>> > There has been very little engagement with the
> issue I
> > referred
> > >>> to. If it was decided that this “check” ought to be
> part
> > of the
> > >>> default checks for R,
> > >>> > then that could have been written to us. Either
> on the
> > >>> bugs.r-project.org <http://bugs.r-project.org>
> <http://bugs.r-project.org <http://bugs.r-project.org>>
> > <http://bugs.r-project.org <http://bugs.r-project.org>
> <http://bugs.r-project.org <http://bugs.r-project.org>>> or the proposed
> > >>> patch. Before we talk about anything else,
> > >>> > it does seem very strange that we cannot get a
> reasonable
> > >>> dialogue going.
> > >>> >
> > >>> > I would like to say that the R/Rust community
> has grown
> > >>> substantially. From my end, there are 3 bindings
> project,
> > extendr,
> > >>> savvy, and roxido.
> > >>> > Then, there are now many rust-based packages on
> CRAN,
> > see this
> > >>> most recent compiled list
> > https://github.com/nanxstats/r-rust-pkgs
> <https://github.com/nanxstats/r-rust-pkgs>
> > <https://github.com/nanxstats/r-rust-pkgs
> <https://github.com/nanxstats/r-rust-pkgs>>
> > >>> <https://github.com/nanxstats/r-rust-pkgs
> <https://github.com/nanxstats/r-rust-pkgs>
> > <https://github.com/nanxstats/r-rust-pkgs
> <https://github.com/nanxstats/r-rust-pkgs>>>.
> > >>> > There is also proof-of-concept
> > >>> https://github.com/r-rust/hellorust
> <https://github.com/r-rust/hellorust>
> > <https://github.com/r-rust/hellorust
> <https://github.com/r-rust/hellorust>>
> > >>> <https://github.com/r-rust/hellorust
> <https://github.com/r-rust/hellorust>
> > <https://github.com/r-rust/hellorust
> <https://github.com/r-rust/hellorust>>> that integrates `cargo`,
> > >>> rust’s official build system, with R’s package
> build system,
> > >>> > and https://github.com/extendr/hellorustc
> <https://github.com/extendr/hellorustc>
> > <https://github.com/extendr/hellorustc
> <https://github.com/extendr/hellorustc>>
> > >>> <https://github.com/extendr/hellorustc
> <https://github.com/extendr/hellorustc>
> > <https://github.com/extendr/hellorustc
> <https://github.com/extendr/hellorustc>>>, which showcases how Rust
> > >>> compiler could be directly linked with R’s package
> system.
> > >>> >
> > >>> > Let me say, that the current R CMD check is
> not meant
> > to be
> > >>> “helpful”. When a package is built, `cargo` tells
> the user
> > >>> “Downloading crates”.
> > >>> > Thus, this information is already conveyed to
> the user.
> > >>> >
> > >>> > Personally, I do wish we could debate this
> requirement
> > further. I
> > >>> do not believe that having R-packages on CRAN
> vendor rust
> > >>> dependencies
> > >>> > as a good policy. Download statistics is a success
> > metric of a
> > >>> given r-package and rust packages. By insisting on
> > vendoring, and
> > >>> thus
> > >>> > side-stepping `cargo` / crates.io
> <http://crates.io> <http://crates.io <http://crates.io>>
> > <http://crates.io <http://crates.io> <http://crates.io
> <http://crates.io>>>, we are
> > >>> robbing upstream authors of their download-numbers.
> I do
> > not think
> > >>> such policy is honourable.
> > >>> >
> > >>> > While C/C++ do not have official package
> repositories,
> > it could
> > >>> be thought of, as fair game, to have CRAN act as a
> pseudo
> > package
> > >>> manager for C/C++ libraries.
> > >>> > I’m not going to argue for or against this part.
> > >>> >
> > >>> > There are many objections from the CRAN side to
> all things
> > >>> related to Rust. I don’t want to open multiple
> topics in
> > the same
> > >>> thread.
> > >>> > But there is plenty to bring up. And I had hoped we
> > could talk
> > >>> this little issue through, before embarking on a larger
> > discussion.
> > >>> > I do not appreciate the “random demands” comment, as
> > this is not
> > >>> a demand, nor is it random.
> > >>> > I have inquired my end of the community for
> suggestions
> > >>> > to compile a larger proposal, but then I was afraid
> > that this
> > >>> would be perceived as a big, bulky demand.
> > >>> >
> > >>> > Rust is not C/C++/Java, and the support for Rust
> cannot
> > look like
> > >>> the support for these languages.
> > >>> >
> > >>> >
> > >>> >
> > >>> > From: Simon Urbanek <simon.urbanek using R-project.org>
> > >>> > Date: Sunday, 2 March 2025 at 00.39
> > >>> > To: Mossa Merhi Reimert <mossa using sund.ku.dk
> <mailto:mossa using sund.ku.dk>
> > <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>>
> > >>> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>
> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>>>>
> > >>> > Cc: r-devel using r-project.org
> <mailto:r-devel using r-project.org>
> > <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>>
> <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>
> > <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>>>
> > >>> <r-devel using r-project.org
> <mailto:r-devel using r-project.org> <mailto:r-devel using r-project.org
> <mailto:r-devel using r-project.org>>
> > <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>
> <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>>>>
> > >>> > Subject: Re: [Rd] R CMD check and CRAN's Rust policy
> > >>> > [Du får ikke ofte mails fra
> simon.urbanek using r-project.org <mailto:simon.urbanek using r-project.org>
> > <mailto:simon.urbanek using r-project.org
> <mailto:simon.urbanek using r-project.org>>
> > >>> <mailto:simon.urbanek using r-project.org
> <mailto:simon.urbanek using r-project.org>
> > <mailto:simon.urbanek using r-project.org
> <mailto:simon.urbanek using r-project.org>>>. Få mere at vide om, hvorfor
> > >>> dette er vigtigt, på
> > https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification>
> > <https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification>>
> > >>> <https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification>
> > <https://aka.ms/LearnAboutSenderIdentification
> <https://aka.ms/LearnAboutSenderIdentification>>> ]
> > >>> >
> > >>> > Mossa,
> > >>> >
> > >>> > the issue you cite is lacking any pertinent
> information
> > and it's
> > >>> not even clear why it should be an issue. The check is
> > perfectly
> > >>> justified, it just reports whether a package using rust
> > declares
> > >>> this correctly and where it downloads 3rd party
> content -
> > something
> > >>> that is important to R users in general and not
> related to
> > CRAN. I
> > >>> don't see how any of this is "prohibitive" it just
> calls
> > out what
> > >>> the package is already doing.
> > >>> >
> > >>> > As discussed before, my hope was that the "R"ust
> > community will
> > >>> mature enough to work on proper support. It is not
> clear
> > that it
> > >>> happened yet, but once it does it would make sense
> to talk
> > about
> > >>> support just as we have for C, C++ and Java, so
> certainly that
> > >>> should be the right discussion. However, it will
> have to
> > start with
> > >>> some thinking and a proposal on how the associated
> issues
> > (compiler
> > >>> support, versioning, dependency sources etc.) are to be
> > addressed,
> > >>> as opposed to making random demands. All this has
> nothing
> > to do with
> > >>> CRAN so the issue you mention seems irrelevant to the
> > progress. Also
> > >>> I'd like to know what are the "challenges embedded in R
> > itself".
> > >>> >
> > >>> > Cheers,
> > >>> > Simon
> > >>> >
> > >>> >
> > >>> >> On Mar 2, 2025, at 8:45 AM, Mossa Merhi Reimert via
> > R-devel
> > >>> <r-devel using r-project.org
> <mailto:r-devel using r-project.org> <mailto:r-devel using r-project.org
> <mailto:r-devel using r-project.org>>
> > <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>
> <mailto:r-devel using r-project.org <mailto:r-devel using r-project.org>>>> wrote:
> > >>> >>
> > >>> >> Hello everyone!
> > >>> >>
> > >>> >> I'm Mossa, I'm one of the maintainers of
> extendr, an
> > automated
> > >>> generation of bindings project for
> > >>> >> Rust code, for use in R-packages.
> > >>> >>
> > >>> >> I'm writing to you, as R 4.4.3 was just
> released, and
> > there have
> > >>> not been
> > >>> >> follow-up on an issue important to us. Link to the
> > issue as
> > >>> discussed on r-devel
> > >>> >>
> > https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html>
> >
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html>>
> > >>>
> >
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html>
> >
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html
> <https://stat.ethz.ch/pipermail/r-devel/2024-October/083666.html>>>
> > >>> >>
> > >>> >> A community member has provided a suggestion to a
> > patch here
> > >>> https://github.com/r-devel/r-svn/pull/182
> <https://github.com/r-devel/r-svn/pull/182>
> > <https://github.com/r-devel/r-svn/pull/182
> <https://github.com/r-devel/r-svn/pull/182>>
> > >>> <https://github.com/r-devel/r-svn/pull/182
> <https://github.com/r-devel/r-svn/pull/182>
> > <https://github.com/r-devel/r-svn/pull/182
> <https://github.com/r-devel/r-svn/pull/182>>>, and we have also
> > >>> attempted to bring it up on
> > >>> >> Bugzilla:
> > https://bugs.r-project.org/show_bug.cgi?id=18806
> <https://bugs.r-project.org/show_bug.cgi?id=18806>
> > <https://bugs.r-project.org/show_bug.cgi?id=18806
> <https://bugs.r-project.org/show_bug.cgi?id=18806>>
> > >>> <https://bugs.r-project.org/show_bug.cgi?id=18806
> <https://bugs.r-project.org/show_bug.cgi?id=18806>
> > <https://bugs.r-project.org/show_bug.cgi?id=18806
> <https://bugs.r-project.org/show_bug.cgi?id=18806>>>
> > >>> >>
> > >>> >> TLDR: Default `R CMD check` uses additional
> > CRAN-specific checks
> > >>> for Rust,
> > >>> >> instead of keeping this behind the --as-cran flag.
> > >>> >>
> > >>> >> I would like to say, that there is a growing
> interest
> > in Rust
> > >>> within the R community.
> > >>> >> And generally, Rust becoming a widely adopted
> language
> > within
> > >>> the Python community (including the scientific part
> of that
> > >>> community). It is time to deal with the
> > >>> >> pain points with using Rust in R.
> > >>> >>
> > >>> >> Therefore, I would kindly ask that we have a
> dialogue
> > on how to
> > >>> remedy the issue above first, and how we may deal with
> > other issues
> > >>> going forward. There are both challenges embedded in R
> > itself, and
> > >>> the current CRAN policy for Rust is prohibitive.
> > >>> >>
> > >>> >>
> > >>> >>
> > >>> >> Mossa Merhi Reimert
> > >>> >> Postdoctoral Researcher
> > >>> >>
> > >>> >> K�benhavns Universitet
> > >>> >> Department of Veterinary and Animal Sciences
> > >>> >> Animal Welfare and Disease Control
> > >>> >> Gr�nneg�rdsvej 8
> > >>> >> 1870 Frederiksberg C
> > >>> >> Denmark
> > >>> >>
> > >>> >> +45 35324135
> > >>> >> mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>
> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>>
> > >>> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>
> > <mailto:mossa using sund.ku.dk
> <mailto:mossa using sund.ku.dk>>><mailto:mossa using sund.ku.dk
> <mailto:mossa using sund.ku.dk>
> > <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>>
> > >>> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>
> <mailto:mossa using sund.ku.dk <mailto:mossa using sund.ku.dk>>>>
> > >>> >>
> > >>> >>
> > >>> >> [[alternative HTML version deleted]]
> > >>> >>
> > >>> >> ______________________________________________
> > >>> >> R-devel using r-project.org
> <mailto:R-devel using r-project.org> <mailto:R-devel using r-project.org
> <mailto:R-devel using r-project.org>>
> > <mailto:R-devel using r-project.org <mailto:R-devel using r-project.org>
> <mailto:R-devel using r-project.org <mailto:R-devel using r-project.org>>>
> > mailing list
> > >>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
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> > >>> >
> > >>> > [[alternative HTML version deleted]]
> > >>> >
> > >>> > ______________________________________________
> > >>> > R-devel using r-project.org
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