Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)
Hi Paul,
On 9 July 2023 at 20:11, Paul Gevers wrote:
| On 09-07-2023 18:41, Dirk Eddelbuettel wrote:
| > On 9 July 2023 at 17:40, Paul Gevers wrote:
| > | Did we already discuss that r-cran-ps also seems to be impacted by the
| > | r-base change of the symbols thingy, as can be seen in r-cran-xopen [1].
| >
| > Correct me if I am wrong but the "symbols thingy" was not a change in R 4.2.*
| > to R 4.3.*. It was a change by some packages opting into different behavior.
|
| I don't understand this then. For several packages we're seeing failures
| in testing even if we only use r-base from unstable and everything else
| from testing to run the test. They pass with a rebuild r-cran-fnn and/or
| a rebuild and updated r-cran-ps, and/or r-cran-tibble. (Sorry, in my
| previous message I think I added r-cran-dplyr by mistake, misremembered).
It would be useful to break this down into concrete reproducible examples.
| > | 33s 10. ps:::not_null(.Call("psll_connections", p))
| >
| > Tis would be a bug in r-cran-ps and I think a Breaks may be warranted.
|
| Ok, let's remember this.
|
| > Given
| > that ps always had 'native symbols', maybe testthat changed?
|
| But I think (I would need to check for the autopkgtest fallback) in none
| of the tests, the version of testthat in testing changed between passing
| and failing tests. Would testthat embed something during the build of
| the binaries (from the name, I would assume not)?
I don't think it would do anything _explicit_.
I think what we are seeing is simply 'fragility from some packages with
larger tails'. If you install 'testthat' (presumably just to run tests) you
end up with with 30+ packages loaded (without considering Suggests:). It is
similar with other 'tidyverse' packages (dplyr, tibble, vctrs, ...) are all
part of that.
| > | Same for r-cran-fnn, which impacts r-cran-uwof [2].
I just looked at FNN, it is very narrow package at its core, it gets a bit of
tail via the Suggests of chemometrics.
| > | I think what we should do is add a versioned Breaks in r-base on
| > | <packages-involved-in:r-graphics-engine>, r-cran-ps, r-cran-tibble,
| > | r-cran-dplyr, r-cran-fnn. I think that's the right thing to do for
| >
| > I think it would be best to work out to corresponding package pairings and
| > apply the Breaks to them. If we can.
|
| Sure, lets add the Breaks to the place where it belongs.
|
| > For spacetime and stars I suspect (based on past experience) possible
| > interaction from the underlying graphics libraries.
|
| Good to hear, didn't check yet, but will shortly (geospatial).
It's a complex block. spacetime is one of the older ones using 'sp' (and then
'raster' via Suggests), 'stars' is newer using 'sf'. Sometimes these prefer /
work better with a consistent rebuild.
| > If I am not mistaken all of these were already in the Excuses list before we
| > made addition of the r-graphics-engine-* tag (which was taken care of for R
| > 4.3.* already, having it may help if another change happens like that).
|
| Sure, I'd hope the r-graphics-engine-* Provides only reduced issue, so
| I'm currently considering them to be different. But I might be proven
| wrong easily.
I don't think it had a net effect this. The
|
| > Unfortunately I find
| > the reports a little hard to read and am hence not very efficient at
| > pinpointing underlying causes. Above you pointed eg at [2] for uwot, I see no
| > error in there :-/
|
| Well, that log has two tests. The first second one passes, the first one
| has:
| 51s > library(testthat)
| 51s > library(uwot)
| 51s Loading required package: Matrix
| 53s >
| 53s > test_check("uwot")
| 53s Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
| 53s Calls: test_check ... eval -> create_data -> find_nn -> FNN_nn ->
| <Anonymous>
| 53s Execution halted
But uwot itself does not force symbols:
https://github.com/jlmelville/uwot/blob/master/src/RcppExports.cpp#L228-L231
and I mentioned, using just those two lines in common. So the forceSymbols
comes from somewhere else.
Ok, I rechecked. R 4.3.0 has this
* Attempting to use a character string naming a foreign function
entry point in a foreign function call in a package will now
signal an error if the packages has called R_forceSymbols to
specify that symbols must be used.
It used to _ignore_ the combinatation of calling R_forceSymbols _and_ use of
non-symbols / quoted identifiers. Now it errors: if you have R_forceSymbols
each .Call() will require symbols (not strings).
So this is where R 4.3.[01] will possibly break with some older packages.
But the fix is simple because when R 4.3.0 came out all packages at CRAN
complied. We need to have current packages that correspond to the R 4.3.0
standard.
(If one were super picky one could call this an ABI/API change and reason for
forcing _all_ packages to be rebuild. I never advocated for that but I am
getting tired of this process. But we need to throw that bomb at some point
just say 'fsck it' and rebuild _all_ packages. Feels like overkill but so is
wasting weeks on this.
| > Obviously, I too want my package r-base in testing and I will help. But I
| > feel that pinning a large Breaks list on it seems a little inefficient /
| > unfair if the package was not causing the change. We can do if there is (as
| > we r-graphics-engine-*) an overwhelming feel "that we must".
|
| I want the Breaks in the right location. If we locate a more logical
| location than r-base, that's where it should go. At least the packages
| involved in the r-graphics-engine would do nice, as it's really the
| change in r-base that broke them (will not be needed anymore after the
(Well, it didn't. It offers a higher API version and it gives packages a
choice to die on that. The six identified package choose to call
R_GE_checkVersionOrDie so they impose a run-time equality on the R engine
they built with. My point is that the accept-vs-break comes from the package,
not from R.)
Dirk
| release of trixie as now we have the Provides): r-cran-cairo,
| r-cran-magick, r-cran-ragg, r-cran-svglite, r-cran-tikzdevice and
| r-cran-vdiffr.
|
| Paul
| x[DELETED ATTACHMENT OpenPGP_signature, application/pgp-signature]
--
dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org
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