[Bioc-devel] DataFrame errors with a Surv class column

[Levi Waldron]

Running and updated Bioc 3.5:

> library(survival)
> set.seed(1)
> cens <- sample(0:1, 100, replace=TRUE)
> time <- rnorm(100)
> df = DataFrame(time=time, cens=cens, y=Surv(time, cens))
> df[1:3, ]  #OK
DataFrame with 3 rows and 3 columns
        time      cens               y.from
   <numeric> <integer>               <Surv>
1  0.3981059         0  0.398105880367068:0
2 -0.6120264         0 -0.612026393250771:0
3  0.3411197         1  0.341119691424425:1
> df #error
DataFrame with 100 rows and 3 columns
*Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds*
>

This came up after I noticed something similar in
MultiAssayExperiment::wideFormat() when trying to reshape a Surv column,
but I'm not sure it's a bug in MultiAssayExperiment:

> library(MultiAssayExperiment)
> miniACC$y <- Surv(miniACC$days_to_death, miniACC$vital_status)
> res = wideFormat(miniACC["EZH2", , ], colDataCols="y")
 Show Traceback

 Rerun with Debug
* Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds *
>

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