[Bioc-devel] Issues with GenomicRanges updates
Nathan Sheffield
nsheff at virginia.edu
Sun Feb 11 04:40:53 CET 2018
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
>>> ```
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
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>>>
>>
>
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