[Bioc-devel] Issues with GenomicRanges updates
Hervé Pagès
hpages at fredhutch.org
Mon Feb 12 20:45:14 CET 2018
Hi Nathan,
You're right, there was a remaining issue. It should be fixed in
IRanges 2.13.26. Make sure to also get S4Vectors 0.17.32 (IRanges
2.13.26 requires it).
The 2 updated packages should become available via biocLite() in
about 24 hours but you can get them now directly from
git.bioconductor.org or from GitHub:
https://github.com/Bioconductor/S4Vectors
https://github.com/Bioconductor/IRanges
Thanks for reporting this and sorry for the inconvenience.
H.
On 02/12/2018 04:28 AM, Nathan Sheffield wrote:
> 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
>>>>> ```
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
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>>>>>
>>>>
>>>
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>>
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>
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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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