[Bioc-devel] Issues with GenomicRanges updates

Hervé Pagès hpages at fredhutch.org
Sun Feb 11 00:19:25 CET 2018


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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> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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