R devel - Jan 2025 - Depends: R (>= 4.1) for packages that use |> and \(...)

Hello all,

Would packages using the underscore placeholder with the native pipe need
to also depend on R >= 4.2.0?

There appear to be a number, modifying Ivan's GitHub search:
https://github.com/search?q=org%3Acran+path%3A%2F%5B.%5D%5BRr%5Dd%3F%24%2F+%2F%5Cs%5C%7C%3E%5Cs.*%3D%5Cs%3F_%2F&type=code

Regards,
Ian
____
Ian Farm
Laboratory Manager, The Agroecology Lab
University of Maine School of Food and Agriculture
5762 Roger Clapp Greenhouses, Orono, Maine 04469


On Wed, Jan 22, 2025 at 1:47?AM Kurt Hornik <Kurt.Hornik at wu.ac.at>
wrote:
> >>>>> Kurt Hornik writes:
>
> I just committed c8761[2-4] to the trunk which adds an internal utility
> for finding package code using the pipe or function shorthand, teaches R
> CMD build to add a dependency on R >= 4.1.0 as necessary, and teaches R
> CMD check to NOTE a missing dependency on R >= 4.1.0, based on
Ivan's
> code.
>
> Currently, we seem to have about 1149 packages on CRAN with package code
> using the pipe or function shorthand, with only 415 depending on R >>
4.1.0, and 734 not.  Argh.
>
> Thanks again for spotting this.
>
> Best
> -k
>
> >>>>> Kurt Hornik writes:
> > Oh dear.  Using a variant of Ivan's code, I seem to find 728 (!!!)
CRAN
> > packages which are missing their R >= 4.1 dependency.
>
> > So clearly we need to do more about this than teach R CMD build to add
> > the dependency ...
>
> > Best
> > -k
>
> >>>>> Henrik Bengtsson writes:
> >> Thanks.  Will take a look ...
>
> >> Best
> >> -k
>
> >>> Thanks for looking into this and the patch. FWIW, there's
an open
> >>> PR18105 - "R CMD build: Add dependency on R >= 4.1.0
if code uses pipe
> >>> symbol |>" for this
> >>> (https://bugs.r-project.org/show_bug.cgi?id=18105).
>
> >>> /Henrik
>
> >>> On Thu, Jan 16, 2025 at 3:42?AM Ivan Krylov via R-devel
> >>> <r-devel at r-project.org> wrote:
> >>>>
> >>>> Hello R-devel,
> >>>>
> >>>> Approximately [*] the following CRAN packages make use of
the pipe
> >>>> syntax in their source code or examples without depending
on R >= 4.1:
> >>>>
> >>>> [1] "biplotEZ"          
"CaseBasedReasoning" "collinear"
> >>>> [4] "cubble"             "disk.frame" 
"duckdbfs"
> >>>> [7] "eia"                "feltr"      
"flattabler"
> >>>> [10] "geodimension"       "hgnc"      
"himach"
> >>>> [13] "lay"                "lidR"      
"locateip"
> >>>> [16] "particles"         
"photosynthesis"     "pivotea"
> >>>> [19] "planr"              "rtrek"     
"satres"
> >>>> [22] "sdtmval"            "selenider" 
"sewage"
> >>>> [25] "stminsights"        "tabr"      
"tidygraph"
> >>>> [28] "tidywikidatar"      "USgas"     
"washi"
> >>>> [31] "zctaCrosswalk"
> >>>>
> >>>> Since we have checks in place to automatically set
Depends: R (>> >>>> 2.10.0) for data files compressed with xz
or bzip2 and >= 3.5.0 for
> >>>> data files serialized with format version 3, would it make
sense to
> >>>> automatically add Depends: R (>= 4.1) for such
packages?
> >>>>
> >>>> The patch at the end of this message adds the R version
dependency
> >>>> during R CMD build:
> >>>>
> >>>> R-devel CMD build --no-build-vignettes .
> >>>> * checking for file ?./DESCRIPTION? ... OK
> >>>> * preparing ?biplotEZ?:
> >>>> * checking DESCRIPTION meta-information ... OK
> >>>> * cleaning src
> >>>> * checking vignette meta-information ... OK
> >>>> * checking for LF line-endings in source and make files
and shell
> >>>> scripts
> >>>> * checking for empty or unneeded directories
> >>>> NB: this package now depends on R (>= 4.1.0)
> >>>> WARNING: Added dependency on R >= 4.1.0 because some of
the source
> >>>> files use the new syntax constructs.
> >>>> Files making use of R >= 4.1 pipe |> or function
shorthand \(...):
> >>>> biplotEZ/R/biplot.R biplotEZ/R/translate_axes.R
> >>>> * building ?biplotEZ_2.2.tar.gz?
> >>>>
> >>>> A more extensive test could also look at the tests, demos,
and
> >>>> \examples{}, but that may take longer and open the door
for false
> >>>> positives. A package that uses |> in one example would
still be useful
> >>>> on R-4.0.0, while a package that uses |> in the source
code would fail
> >>>> to parse and install.
> >>>>
> >>>> Index: src/library/tools/R/QC.R
> >>>>
==================================================================>
>>>> --- src/library/tools/R/QC.R    (revision 87545)
> >>>> +++ src/library/tools/R/QC.R    (working copy)
> >>>> @@ -10367,7 +10367,29 @@
> >>>> }
> >>>> }
> >>>>
> >>>> +.check_use_of_R41_syntax <-
> >>>> +function(files)
> >>>> +{
> >>>> +    out <- vapply(files,
> >>>> +           function(f) tryCatch(
> >>>> +               any(getParseData(parse(f, keep.source =
TRUE))$token
> %in% c("PIPE", "'\\\\'")),
> >>>> +               error = function(e) FALSE
> >>>> +           ),
> >>>> +           FALSE)
> >>>> +    out <- files[out]
> >>>> +    class(out) <- "check_use_of_R41_syntax"
> >>>> +    out
> >>>> +}
> >>>>
> >>>> +format.check_use_of_R41_syntax <-
> >>>> +function(x, ...)
> >>>> +{
> >>>> +    if (length(x)) {
> >>>> +        c("Files making use of R >= 4.1 pipe
|> or function
> shorthand \\(...):",
> >>>> +          .strwrap22(x, " "))
> >>>> +    } else character()
> >>>> +}
> >>>> +
> >>>> ### Local variables: ***
> >>>> ### mode: outline-minor ***
> >>>> ### outline-regexp: "### [*]+" ***
> >>>> Index: src/library/tools/R/build.R
> >>>>
==================================================================>
>>>> --- src/library/tools/R/build.R (revision 87545)
> >>>> +++ src/library/tools/R/build.R (working copy)
> >>>> @@ -1165,9 +1165,11 @@
> >>>> desc <- .read_description(file.path(pkgname,
"DESCRIPTION"))
> >>>> Rdeps <- .split_description(desc)$Rdepends2
> >>>> hasDep350 <- FALSE
> >>>> +        hasDep410 <- FALSE
> >>>> for(dep in Rdeps) {
> >>>> if(dep$op != '>=') next
> >>>> if(dep$version >= "3.5.0") hasDep350 <-
TRUE
> >>>> +            if(dep$version >= "4.1.0")
hasDep410 <- TRUE
> >>>> }
> >>>> if (!hasDep350) {
> >>>> ## re-read files after exclusions have been applied
> >>>> @@ -1189,6 +1191,23 @@
> >>>> "\n")
> >>>> }
> >>>> }
> >>>> +        if (!hasDep410) {
> >>>> +            uses410 <-
> .check_use_of_R41_syntax(dir(file.path(pkgname, "R"),
> >>>> +                                                   
full.names > TRUE,
> >>>> +                                                   
pattern > "[.]R$",
> >>>> +                                                   
ignore.case > TRUE))
> >>>> +            if (length(uses410)) {
> >>>> +                fixup_R_dep(pkgname, "4.1.0")
> >>>> +                msg <- paste("WARNING: Added
dependency on R >> 4.1.0 because",
> >>>> +                             "some of the source
files use the new
> syntax",
> >>>> +                             "constructs.")
> >>>> +                printLog(Log,
> >>>> +                         paste(c(strwrap(msg, indent =
2L, exdent > 2L),
> >>>> +                                 format(uses410)),
> >>>> +                               collapse =
"\n"),
> >>>> +                               "\n")
> >>>> +            }
> >>>> +        }
> >>>>
> >>>> ## add NAMESPACE if the author didn't write one
> >>>> if(!file.exists(namespace <- file.path(pkgname,
"NAMESPACE")) ) {
> >>>>
> >>>>
> >>>> --
> >>>> Best regards,
> >>>> Ivan
> >>>>
> >>>> [*] Based on the following GitHub search, which requires
logging in:
> >>>>
>
https://github.com/search?q=org%3Acran%20path%3A%2F%5B.%5D%5BRr%5Dd%3F%24%2F%20%2F%5Cs%5C%7C%3E%2F&type=code
> >>>> There's currently no REST API support for regexp
search, so the list
> >>>> was obtained manually.
> >>>>
> >>>> ______________________________________________
> >>>> R-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
	[[alternative HTML version deleted]]

Many thanks to Henrik for remembering the report in Bugzilla and to
Kurt for implementing the change and finding out the true number of
affected packages.

On Wed, 22 Jan 2025 15:34:41 -0500
Ian Farm <ian.farm at maine.edu> wrote:
> Would packages using the underscore placeholder with the native pipe
> need to also depend on R >= 4.2.0?
That's a good find! For the R >= 4.2 syntax, we only need to check for
getParseData(...)$token %in% 'PLACEHOLDER'. The R >= 4.3 syntax
feature
is harder to test for:
>> As an experimental feature the placeholder _ can now also be used in
>> the rhs of a forward pipe |> expression as the first argument in an
>> extraction call, such as _$coef. More generally, it can be used as
>> the head of a chain of extractions, such as _$coef[[2]]. 
I think it might be possible to parse(text = paste('PLACEHOLDER |>',
grandparent_expression)) and then look at the top-level function in the
call, but that feels quite fragile:

x <- utils::getParseData(parse(f, keep.source = TRUE))
i <- x$token %in% "PLACEHOLDER"
pi <- x[i, "parent"]
ppi <- x[x$id %in% pi, "parent"]
placeholder_expressions <- utils::getParseText(x, ppi)
extractor_used <- vapply(placeholder_expressions, function(src) {
 toplevel <- parse(text = paste("PLACEHOLDER |> ",
src))[[1]][[1]]
 identical(toplevel, quote(`$`)) ||
  identical(toplevel, quote(`[`)) ||
  identical(toplevel, quote(`[[`))
}, FALSE)

Alternatively, we may find the first child of the grandparent of the
placeholder. If it's the placeholder expression, then the pipe must be
of the form ...|> _..., which is the R >= 4.3 syntax:

x <- utils::getParseData(parse(f, keep.source = TRUE))
i <- x$token %in% "PLACEHOLDER"
vapply(which(i), function(i) {
 pi <- x[i, "parent"]
 ppi <- x[x$id %in% pi, "parent"]
 cppi <- x[x$parent %in% ppi, "id"]
 min(cppi) == pi
}, FALSE)

-- 
Best regards,
Ivan