Fixed duplicate column names in `merge()` when by.x in names(y)

[sritchie73]

When joining two data.tables using merge() the resulting data.table will contain duplicate column names if by.x != by.y and by.x is also in names(y).

An example:

# Create example data.frames
parents <- data.table(name=c("Sarah", "Max", "Qin", "Lex"), 
                      sex=c("F", "M", "F", "M"), 
                      age=c(41, 43, 36, 51))
children <- data.table(parent=c("Sarah", "Max", "Qin"), 
                       name=c("Oliver", "Sebastian", "Kai-lee"),
                       sex=c("M", "M", "F"), 
                       age=c(5,8,7))

# Merge() creates a duplicated "name" column:
merge(parents, children, by.x = "name", by.y = "parent")

Output:

   name sex.x age.x      name sex.y age.y
1   Max     M    43 Sebastian     M     8
2   Qin     F    36   Kai-lee     F     7
3 Sarah     F    41    Oliver     M     5

This behaviour is also present in base:::merge.data.frame(), but throws an additional warning:

Warning message:
In merge.data.frame(parents, children, by.x = "name", by.y = "parent") :
  column name ‘name’ is duplicated in the result

This patch fixes this problem by checking for names shared between by.x and names(y), and adding the appropriate suffixes to those column names.

[sritchie73]

Also added an equivalent warning message to base for cases when duplicate column names are returned. With the patch above, the only way this can happen is if the user supplies identical values to the suffixes argument (e.g. suffixes=c("", "")).

[HughParsonage]

Trailing , should be removed.

[sritchie73]

RE: failed checks: I can't work out how to write the test that checks for the appropriate warning message - would appreciate advice here since there's no documentation for data.table:::test().

I also can't run the tests on my local machine because the package fails to compile (I don't have OpenMP).

[mattdowle]

Looks good. On test(), search tests.Rraw for warning= to see other examples in other tests to follow. You can also pass output= and/or error= to search for patterns in those messages.
It should compile ok without OpenMP as it should detect if OpenMP is available and switch out. How are you compiling and what is the message it fails with at what point? This is my dev cycle: cc.R and Pasha added a Makefile (both linked in item 8 here).

[codecov-io]

Codecov Report

Merging #2631 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2631      +/-   ##
==========================================
+ Coverage   93.13%   93.14%   +<.01%     
==========================================
  Files          61       61              
  Lines       12120    12130      +10     
==========================================
+ Hits        11288    11298      +10     
  Misses        832      832

Impacted Files	Coverage Δ
R/merge.R	94.73% <100%> (+0.79%)	⬆️

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[sritchie73]

Thanks @mattdowle, I couldn't get the package to build using RStudio package build system - but I probably have something misconfigured in my environment. I was able to get the tests to work with a bit of trial and error.

[MichaelChirico]

I added a little bit to the Contributing wiki to make it a bit easier to understand how the testing regime works. Thanks for the PR.

[MarkusBonsch]

I love it, although it breaks consistency with merge.data.frame. There are quite some other issues with merge.data.table at the moment (#2593). Once these are all fixed (I am working on it), we have to update the documentation to clearly reflect, where we have differences to merge.data.frame.

[MichaelChirico]

@sritchie73 I assume the Rstudio issue is the same as #2585. I've been using the command line to re-install lately

[sritchie73]

Thanks @MarkusBonsch , for what its worth I've also sent a similar patch to the R-devel mailing list for merge.data.frame - but the two people who responded (neither core dev team) were pessimistic about my chances of getting the patch accepted.

@MichaelChirico I get a different error:

==> R CMD INSTALL --no-multiarch --with-keep.source data.table

* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘data.table’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c assign.c -o assign.o
clang: error: unsupported option '-fopenmp'
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/data.table’

Exited with status 1.

In the end I managed to get data.table:::test() working almost the same way in my local R session, by copying the file preamble, then fixed the remaining issues that came up in Travis after pushing the changes out to my branch.

[jangorecki]

If this PR makes merge.data.table to be less consistent to data.frame method then please describe that in manual. You can link your R-devel patch there also so we (anyone) can track it later on if it happens to be merged to R-devel.

[sritchie73]

Here is the thread on R-devel: http://r.789695.n4.nabble.com/Duplicate-column-names-created-by-base-merge-when-by-x-has-the-same-name-as-a-column-in-y-td4748345.html

There is now a suggestion of just adding the suffix to the column name in y to keep backwards compatibility (i.e. any by.x column can still be referred to by its original name). If that patch is accepted I can similarly update merge.data.table to have this behaviour also.

[jangorecki]

LGTM. You sometimes use paste(, sep="") and another time paste0, as we now depends on R 3.1 we can safely use paste0, but this is minor thing. We can wait a little bit and see what R-devel will decide.

[sritchie73]

Thanks @jangorecki - I had used paste rather than paste0 in the first instance to match the code style for the existing suffix handling which immediately precedes my patch. Would you prefer I change it to paste0, or keep it consistent with the code preceding it?

[jangorecki]

Lets wait for R-devel, paste is not that important

[mattdowle]

Given Martin Maechler's reply today, it's looking likely to be accepted for R. Wow! Well navigated! I updated manual page accordingly (including link to thread too as Jan suggested) and will merge.
Will invite you to be project member too.

[sritchie73]

Thanks!

I am following up with Martin to clarify the functionality of the proposed no.dups argument so we can mirror the behaviour of merge.data.frame.