[Bioc-devel] Duplicated method names in purrr and GenomicRanges

[Henrik Bengtsson]

Just an FYI, *if* all you're doing is rbind():ing those data frames,
then you're better of doing:

  df <- do.call(rbind, dfs)

than

  df <- Reduce(rbind, dfs)

because the former is faster and more memory efficient:

> dfs <- rep(list(iris), times=100)
> bench::mark(df <- Reduce(rbind, dfs))[,1:7]
# A tibble: 1 x 7
  expression                    min   median `itr/sec` mem_alloc `gc/sec` n_itr
  <bch:expr>               <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl> <int>
1 df <- Reduce(rbind, dfs)   65.5ms   68.6ms      13.6     108MB     30.7     8
Warning message:
Some expressions had a GC in every iteration; so filtering is disabled.

> bench::mark(df <- do.call(rbind, dfs))[,1:7]
# A tibble: 1 x 7
  expression                     min   median `itr/sec` mem_alloc `gc/sec` n_itr
  <bch:expr>                <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl> <int>
1 df <- do.call(rbind, dfs)   8.67ms   9.47ms      105.      14MB     49.5    34

/Henrik

On Fri, Sep 13, 2019 at 5:39 AM <bioinf using posteo.de> wrote:
>
> Thank you for all of your answers. Michaels solution works fine for me.
> I had to merge a list of data.frames. Used the solution in this thread here:
>
> https://stackoverflow.com/questions/8091303/simultaneously-merge-multiple-data-frames-in-a-list
>
> Am 12.09.19 um 13:05 schrieb Michael Lawrence via Bioc-devel:
> > Third option: use Reduce() from base instead of purr::reduce().
> >
> > On Thu, Sep 12, 2019 at 2:54 AM O'CALLAGHAN Alan
> > <A.B.O'Callaghan using sms.ed.ac.uk> wrote:
> >> Hi,
> >>
> >> Two options.
> >>
> >> First option: import either purrr::reduce or GenomicRanges::reduce, and
> >> call the other with [pkg]::reduce.
> >>
> >> Second option: remove the import for both of these. Use purrr::reduce
> >> and GenomicRanges::reduce to call both functions.
> >>
> >> I think the second option leads to clearer code and would be my definite
> >> preference.
> >>
> >>
> >> On 12/09/2019 10:07, bioinf using posteo.de wrote:
> >>> Dear all,
> >>>
> >>> I am developing a Bioconductor package and have a problem with two
> >>> methods which have the same name. I am using the reduce() function
> >>> from the R packages GenomicRanges and purrr. All methods from other
> >>> packages are imported with @importFrom in all of my functions.
> >>>
> >>>
> >>> During devtools::document() I get the following Warning:
> >>>
> >>> ...
> >>>
> >>> replacing previous import ‘GenomicRanges::reduce’ by ‘purrr::reduce’
> >>> when loading ‘testPackage’
> >>>
> >>> ...
> >>>
> >>>
> >>> Here are my NAMESPACE entries:
> >>>
> >>> # Generated by roxygen2: do not edit by hand
> >>>
> >>> export(mergeDataFrameList)
> >>> export(reduceDummy)
> >>> importFrom(GenomicRanges,GRanges)
> >>> importFrom(GenomicRanges,reduce)
> >>> importFrom(IRanges,IRanges)
> >>> importFrom(dplyr,"%>%")
> >>> importFrom(dplyr,left_join)
> >>> importFrom(dplyr,mutate)
> >>> importFrom(dplyr,pull)
> >>> importFrom(magrittr,"%<>%")
> >>> importFrom(purrr,reduce)
> >>> importFrom(tibble,tibble)
> >>>
> >>>
> >>> I am not using both reduce functions in the same function. To use the
> >>> GenomicRanges reduce function, I have to call this function like this:
> >>> GenomicRanges::reduce().
> >>>
> >>> I understand the warning and why I have to call the reduce function
> >>> like this. Is there a solution for this problem? Compiling a R package
> >>> with warnings and calling functions like this is not the best way I
> >>> guess.
> >>>
> >>> I am using R version 3.6.1 (2019-07-05)
> >>>
> >>> Thanks for help!
> >>>
> >>> Best,
> >>>
> >>> Tobias
> >>>
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> >
>
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