thr3ads.net - R devel - [Rd] Depends: R (>= 4.1) for packages that use |> and \(...) [Jan 2025]

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Ivan Krylov

2025-Jan-16 11:41 UTC

[Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

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.

Henrik Bengtsson

2025-Jan-16 15:22 UTC

head link

[Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

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

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