[Bioc-devel] DataFrame: replacement error

[Ludwig Geistlinger]

I have a SummarizedExperiment with putatively user-annoted rowData.
I have a function that does computation on this SE and appends
the results to the rowData.
When (repeatedly) called on the SE, the function just overwrites / replaces already existing columns.

In R release and S4Vectors_0.20.1

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] S4Vectors_0.20.1    BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] compiler_3.5.2

this works:

# my rowData
> d <- DataFrame(a=c(1,2), b=c(3,4), c=c(5,6))
DataFrame with 2 rows and 3 columns
          a         b         c
  <numeric> <numeric> <numeric>
1         1         3         5
2         2         4         6

# output of my function
> d2 <- DataFrame(b=c(7,8), c=c(9,10), d=c(11,12))
DataFrame with 2 rows and 3 columns
          b         c         d
  <numeric> <numeric> <numeric>
1         7         9        11
2         8        10        12

# replace and simultaneously append
> d[,colnames(d2)] <- d2
> d
DataFrame with 2 rows and 4 columns
          a         b         c         d
  <numeric> <numeric> <numeric> <numeric>
1         1         7         9        11
2         2         8        10        12




However, using R-devel and S4Vectors_0.21.20

> sessionInfo()
R Under development (unstable) (2019-01-18 r75994)
Platform: x86_64-apple-darwin18.2.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /Users/ludwig/Downloads/R-devel/lib/libRblas.dylib
LAPACK: /Users/ludwig/Downloads/R-devel/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] S4Vectors_0.21.20   BiocGenerics_0.29.2

loaded via a namespace (and not attached):
[1] compiler_3.6.0


The same replacement operation causes an error

> d[,colnames(d2)] <- d2
Error in names(x using listData) <- value :
  'names' attribute [3] must be the same length as the vector [1]


For data.frame, this still works in R-devel:
> dd <- as.data.frame(d)
> dd2 <- as.data.frame(d2)
> dd[,colnames(dd2)] <- dd2
> dd
  a b  c  d
1 1 7  9 11
2 2 8 10 12

How to best address this issue?


--
Dr. Ludwig Geistlinger
CUNY School of Public Health

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