S4Vectors

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`cumsum` tolerates empty elements in a `RleList` unless the empty element is in terminal position… ``` > RleList(Rle(), Rle(1), Rle(1)) |> cumsum() RleList of length 3 [[1]] numeric-Rle of length...

charles-plessy

`[` fails when the condition contains `NAs`

5

Hi there, I have an issue related with the `[` which is not consistent with the base R. Normally, when one pass the condition containing NAs into `[`, NAs will...

gogonzo

Native support for groupInfo slot

8

I propose enabling native support for group information and submit a draft implementation. One of the advantages of `dplyr` and `tibble` is support for groupwise operations. `dplyr` stores a `tbl_df`...

jonocarroll

Should SimpleList inherit list?

1

Suggested by Charles Plessy on the [Bioconductor support site](https://support.bioconductor.org/p/9141088/). Could be something like this (roughly): ``` library(S4Vectors) setClass("SimpleList2", contains=c("List", "list")) setMethod("parallel_slot_names", "SimpleList2", function(x) c(".Data", callNextMethod())) setMethod("as.list", "SimpleList2", function(x) setNames([email protected], names(x)))...

hpages

merging DFrames

4

This issue is a follow up to [this](https://stat.ethz.ch/pipermail/bioc-devel/2020-October/017383.html) email on the bioc-devel mailing list. When merging DFrame instances, the *List types are lost: The following two instances have NumericList columns...

lgatto

Cryptic error message from subsetByOverlaps, maybe related to recent update to extractROWS?

2

My CAGEfightR package has recently produced a cryptic error message on the Bioconductor servers, that I cannot myself reproduce: ``` Running examples in ‘CAGEfightR-Ex.R’ failed The error most likely occurred...

MalteThodberg

Consider: ```r library(S4Vectors) X

LTLA

I have several applications where I have a matrix or a vector and I just want to slap some metadata on them without changing the object. To this end, I...

LTLA

undesirable promotion of SimpleLists to subclasses by endoapply

2

Consider the following example: ```r library(S4Vectors) hits

LTLA

rev on DataFrame does not reverse column order, as it does on data.frame

4

Perhaps I should infer this from the documentation. Or it is natural consequence from underlying implementation. Or perhaps it is an unintentional behavior. Can I get a witness? Is there...

malcook