[Bioc-devel] Issues with GenomicRanges updates
Nathan Sheffield
nathan at code.databio.org
Sun Feb 11 01:33:03 CET 2018
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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>
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