[Bioc-devel] Issues with GenomicRanges updates
Nathan Sheffield
nsheff at virginia.edu
Mon Feb 12 13:28:49 CET 2018
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
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FrZj-JCIQePYSae83Zo7pEJhLJDjFiRPOmff3fGshM4&s=dO7xndrTgL8lx8igvje5h0wKEFwaH0hwLq04G5UNcRs&e=
>>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
More information about the Bioc-devel
mailing list