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[R-pkg-devel] Removing import(methods) stops exporting S4 "meta name"

4 messages · Michael Chirico, Duncan Murdoch, Richard M. Heiberger +1 more

Original
Michael Chirico
# 
In an effort to streamline our NAMESPACE, we moved from blanket
'import(methods)' to specific importFrom(methods, ....) for the
objects we specifically needed.

Doing so broke a downstream package, however, which has this directive:

importFrom(data.table,`.__T__[:base`)

That package stopped installing after the above change. I can get it
to install again by adding:

importClassesFrom(methods, "[")

to our package, but I'm not sure why this would be necessary. I'm
still left with two questions:

 1. How did we end up with ".__T__[:base" in our exports when we don't
do any S4 around '[' in the package (we do export S3 methods on it)?
 2. Is there any legitimate reason for a package to try and import
such an object? In other words, is breaking this downstream package by
not adding the 'importClassesFrom' workaround the right thing to do? I
don't see any other CRAN packages with a similar directive in its
NAMESPACE.

Michael Chirico
Duncan Murdoch
# 
To save others a bit of time, the package in question is "do", and 
Michael has already posted an issue on their Github page asking why they 
made this import:  https://github.com/yikeshu0611/do/issues/1 .

And if you remove that import and run R CMD check on "do", it fails with 
this error:

* checking examples ... ERROR
Running examples in ?do-Ex.R? failed
The error most likely occurred in:

 > ### Name: join
 > ### Title: Join two dataframes together
 > ### Aliases: join join_inner join_full join_left join_right join_out
 >
 > ### ** Examples
 >
 > df1=data.frame(x=rep(c('b','a','c'),each=3),
+               y=c(1,3,6),
+               v=1:9)
 >
 > df2=data.frame(x=c('c','b','e'),
+                v=8:6,
+                foo=c(4,2,1))
 > join_inner(df1,df2,'x')
Error in xj[i] : invalid subscript type 'list'
Calls: join_inner -> data.frame -> [ -> [.data.table -> [.data.frame
Execution halted

I'm pretty sure that import should not be made, but I don't know the 
intention of this example, or what the correct fix would be.

Duncan Murdoch
On 14/03/2024 2:34 p.m., Michael Chirico wrote:
Richard M. Heiberger
# 
this looks like a relative of the issue I tripped on that is discussed in the email threads

https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010531.html

https://stat.ethz.ch/pipermail/r-devel/2024-March/083259.html

At issue is the default export of
exportPattern(".") 

System generated names, which is what ".__xxx__" looks like, seem to be the issue.
I can't make any specific recommendations behind connecting this current issue to my recent experience.

Rich
Ivan Krylov
# 
On Thu, 14 Mar 2024 16:06:50 -0400
Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

            

      
      
      
    

        
And here's how it happens:

join_inner calls xi[yi,on=by,nomatch=0] on data.tables xi and yi.

`[.data.table` calls cedta() to determine whether the calling
environment is data.table-aware. If the import of `.__T__[:base` is
removed, cedta() returns FALSE.

`[.data.table` then forwards the call to `[.data.frame`, which cannot
handle data.table-style subsetting.

This is warned about in
<https://cran.r-project.org/package=data.table/vignettes/datatable-importing.html#data-table-in-imports-but-nothing-imported>;
the 'do' package should have set the .datatable.aware = TRUE marker in
its environment. In fact, example(join_inner) doesn't raise an error
with the following changes when running with data.table commit f92aee69
(i.e. pre-#6001):

diff -rU2 do/NAMESPACE do_2.0.0.0.2/NAMESPACE
--- do/NAMESPACE	2021-08-03 12:37:00.000000000 +0300
+++ do_2.0.0.0.2/NAMESPACE	2024-03-15 14:01:10.588561222 +0300
@@ -130,5 +130,4 @@
 export(upper.dir)
 export(write_xlsx)
-importFrom(data.table,`.__T__[:base`)
 importFrom(methods,as)
 importFrom(reshape2,melt)
diff -rU2 do/R/join.R do_2.0.0.0.2/R/join.R
--- do/R/join.R	2020-06-30 06:47:22.000000000 +0300
+++ do_2.0.0.0.2/R/join.R	2024-03-15 13:54:02.289440613 +0300
@@ -1,2 +1,4 @@
+.datatable.aware = TRUE
+
 #' @title Join two dataframes together
 #' @description Join two dataframes by the same id column.