[Bioc-devel] Issues with GenomicRanges updates

[Nathan Sheffield]

I'm having some issues getting my package LOLA to pass R CMD check using 
the updated dev versions of GenomicRanges et al.

It seems like any time I try to apply something across a 
"CompressedGRangesList" object, it's giving errors when I use mclapply 
from parallel. Here's a reproducible example:

data("sample_input", package="LOLA")
library(parallel)
mclapply(userSets, length)

(loads packages...)

Error in lapply_CompressedList(X, FUN, ...) :
   invalid output element of class "GRanges"


It works with regular lapply:

 > lapply(userSets, length)
$setA
[1] 3142

$setB
[1] 5831


This is running on the bioconductor docker devel_core2 container, and 
I've then gone and updated to the latest dev versions of these packages 
with `biocLite()`.

I earlier ran into issues using `as.list()` on these same 
CompressedGRangesList objects. It used to be that I had to call as.list 
when they were just GRangesList objects, but now that's failing, and so 
I've had to go take all calls to as.list out of my code. This has solved 
that issue (I guess the updates made the as.list calls unnecessary), but 
you can see it's still causing errors:

as.list(userSets)
Error in lapply_CompressedList(X, FUN, ...) :
   invalid output element of class "GRanges"

-Nathan

```
 > sessionInfo()
R Under development (unstable) (2018-02-04 r74204)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicRanges_1.31.18 GenomeInfoDb_1.15.5 IRanges_2.13.24
[4] S4Vectors_0.17.31     BiocGenerics_0.25.3

loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0        compiler_3.5.0 XVector_0.19.8
[4] tools_3.5.0            GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
```