Issue with aggregate command (from stats) in notebooks only

[etabeta78]

Jupyter notebooks with R kernel seem to have issues in some cases when aggregate (from stats package in base R) returns multiple values (e.g. a vector).

This can be reproduced by running the following command

aggregate(. ~ Species, iris, range)

which results in an error:

ERROR while rich displaying an object: Error in vapply(part, format, character(nrow(part))): values must be length 3, but FUN(X[[2]]) result is length 6

The issue is mitigated by the fact that if I run

aggregate(. ~ Species, iris, range, simplify=F)

the code works, but this way I get a data.frame with list columns and not the same object that I can obtain from R console with simplify=T (default value).

The issue seems strictly related either to the way IRkernel tries to display the data.frame, since the command

print(aggregate(. ~ Species, iris, range))

produce the correct output. But it surprised me that the code works flawlessly in R and Rmarkdown and it fails on IRkernel notebooks

I was unable to find a similar issue on the github tracker (searching for vapply and aggregate or print), so I hope this is not a duplicated report.

My system has:

• R 3.5.1
• IRkernel_0.8.15.9000
• IRdisplay_0.7.0
• repr_0.19.2

but the issue is reproducible also on my colleague laptop.

[flying-sheep]

That’s a super weird structure.

> str(aggregate(. ~ Species, iris, range))
 'data.frame':	3 obs. of  5 variables:
 $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 2 3
 $ Sepal.Length: num [1:3, 1:2] 4.3 4.9 4.9 5.8 7 7.9
 $ Sepal.Width : num [1:3, 1:2] 2.3 2 2.2 4.4 3.4 3.8
 $ Petal.Length: num [1:3, 1:2] 1 3 4.5 1.9 5.1 6.9
 $ Petal.Width : num [1:3, 1:2] 0.1 1 1.4 0.6 1.8 2.5

A data frame with matrices as columns?

Hmm, no idea how to do that best.

[etabeta78]

Thanks a lot for taking a look (and for moving it in the proper component repo)!

Base R coerces the matrix columns to separate data.frame columns, appending a column-in-matrix index to the column main name (i.e. you get Sepal.Length.1 & Sepal.Length.2 and so on)...

This happens with any kind of multivalued function passed through aggregate, for what is worth:
range is simply the easiest reproducible case I found

[flying-sheep]

Base R coerces the matrix columns to separate data.frame columns

Yes, for printing. Doesn’t seem like a good idea: People will think df$Sepal.Width.1 is an actual column and will get confused when it isn’t.

I’m thinking that we could handle it by collapsing the rows of the nested matrices with commas:

Species	Sepal.Length	Sepal.Width
setosa	4.3, 5.8	2.3, 4.4
versicolor	4.9, 7.0	2.0, 3.4

[etabeta78]

That would be like forcing simplify=F for situations where the simplification triggers vapply errors: I think it is absolutely reasonable :-)

[etabeta78]

Thanks a lot!