Hi Herve,

The updates have indeed solved those issues for that sample -- However, when you try to apply a more complicated function, I am getting the same error. Here's a reproducible example of the error again, this time using the latest GenomicRanges and IRanges packages:


library(GenomicRanges)
data("sample_input", package="LOLA")
as.list(userSets)
lapply(userSets, length)

# That works now


data("sample_universe", package="LOLA")

f = function(x, userUniverse) {
        fo = findOverlaps(x, userUniverse)
        y = userUniverse[unique(subjectHits(fo))]
        return(y)
 }

lapply(userSets, f, userUniverse)

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


This works under earlier versions. Can you see if this fails in your setup? Or am I doing something strange in the function? Here's my sessionInfo showing I updated to the latest packages:

-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] parallel  stats4    stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5   IRanges_2.13.25
[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 tools_3.5.0
[4] XVector_0.19.8         GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6

On 02/10/2018 10:40 PM, Nathan Sheffield wrote:
Hi Herve,

Never mind, I see now I am still a day old, looks like I was looking at your sessionInfo paste and thought it was mine, whoops. I'll give it another try tomorrow with the new versions.

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

-Nathan

On 02/10/2018 07:33 PM, Nathan Sheffield wrote:
According to my `sessionInfo` (see below), those are the versions I had been using:

other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5   IRanges_2.13.25
[4] S4Vectors_0.17.31     BiocGenerics_0.25.3

And I had pulled them from biocLite...what's going on?

-Nathan


On 02/10/2018 06:19 PM, Hervé Pagès wrote:
Hi Nathan,

I can't reproduce this with the latest versions of S4Vectors (0.17.31),
IRanges (2.13.25), and GenomicRanges (1.31.19). Note that these versions
will only become available via biocLite() tomorrow but you can get them
directly from git.bioconductor.org.

With these versions, as.list, lapply, and mclapply work for on userSets:

  > library(GenomicRanges)
  > data("sample_input", package="LOLA")
  > as.list(userSets)
  $setA
  GRanges object with 3142 ranges and 0 metadata columns:
           seqnames               ranges strand
              <Rle>            <IRanges> <Rle>
       [1]     chr1   [ 437151,  438164]      *
       [2]     chr1   [ 875730,  878363]      *
       [3]     chr1   [ 933387,  937410]      *
       [4]     chr1   [ 967966,  970238]      *
       [5]     chr1   [1016863, 1017439]      *
       ...      ...                  ...    ...
    [3138]     chrY [ 9364545,  9364859]      *
    [3139]     chrY [ 9385471,  9385777]      *
    [3140]     chrY [14532115, 14533600]      *
    [3141]     chrY [23696580, 23696878]      *
    [3142]     chrY [26959489, 26959716]      *
    -------
    seqinfo: 69 sequences from an unspecified genome; no seqlengths

  $setB
  GRanges object with 5831 ranges and 0 metadata columns:
           seqnames               ranges strand
              <Rle>            <IRanges> <Rle>
       [1]     chr1     [ 28735,  29810]      *
       [2]     chr1     [544738, 546649]      *
       [3]     chr1     [713984, 714547]      *
       [4]     chr1     [762416, 763445]      *
       [5]     chr1     [805198, 805628]      *
       ...      ...                  ...    ...
    [5827]     chrY [20508190, 20508452]      *
    [5828]     chrY [21154603, 21155040]      *
    [5829]     chrY [21238448, 21240005]      *
    [5830]     chrY [26979889, 26980116]      *
    [5831]     chrY [28773315, 28773544]      *
    -------
    seqinfo: 69 sequences from an unspecified genome; no seqlengths

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

  $setB
  [1] 5831

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

  $setB
  [1] 5831

Note that you should not need to call as.list() on a GRangesList object
before passing it to lapply() or mclapply().

Let me know if the problem persist after you update.

Best,
H.

> sessionInfo()
R Under development (unstable) (2017-12-11 r73889)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /home/hpages/R/R-3.5.r73889/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r73889/lib/libRlapack.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=en_US.UTF-8
 [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] parallel  stats4    stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[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         tools_3.5.0
[4] XVector_0.19.8         GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6


On 02/10/2018 02:48 PM, Nathan Sheffield wrote:
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
```

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