[Bioc-devel] Merging two CharacterList objects doesn't work in Bioc-devel
Hervé Pagès
hpages at fredhutch.org
Sat Sep 10 11:47:56 CEST 2016
Hi Leonardo,
Not really intended. Should be addressed in S4Vectors 0.11.14.
Cheers,
H.
On 09/08/2016 12:14 PM, Leonardo Collado Torres wrote:
> Hi,
>
> With Bioc-release I can run without problems the following code:
>
> library('GenomicRanges')
> l <- CharacterList(list(NA, NA, '1', '2'))
> r <- CharacterList(as.list(letters[1:4]))
> tmp <- merge(l, r, all = TRUE)
>
> However, it gives an error with Bioc-devel:
>
> Error in V_recycle(value, x, x_what = "value", skeleton_what = "x") :
> 'NROW(value)' is 0 but 'length(x)' is not
> In addition: Warning messages:
> 1: In if (any(duplicated(object))) warning(wmsg("Some of the objects
> to merge contain ", :
> the condition has length > 1 and only the first element will be used
> 2: In if (any(duplicated(object))) warning(wmsg("Some of the objects
> to merge contain ", :
> the condition has length > 1 and only the first element will be used
>
>
> Is this intended?
>
> Best,
> Leo
>
>
>
> Bioc-release info:
>
>> library(GenomicRanges)
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
> duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
> is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
> paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
> Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unsplit
>
> Loading required package: S4Vectors
> Loading required package: stats4
>
> Attaching package: ‘S4Vectors’
>
> The following objects are masked from ‘package:base’:
>
> colMeans, colSums, expand.grid, rowMeans, rowSums
>
> Loading required package: IRanges
> Loading required package: GenomeInfoDb
>> l <- CharacterList(list(NA, NA, '1', '2'))
>> r <- CharacterList(as.list(letters[1:4]))
>> tmp <- merge(l, r, all = TRUE)
>> tmp
> group group_name value
> 1 1 <NA> a
> 2 1 <NA> <NA>
> 3 2 <NA> b
> 4 2 <NA> <NA>
> 5 3 <NA> 1
> 6 3 <NA> c
> 7 4 <NA> 2
> 8 4 <NA> d
>> options(width = 120); devtools::session_info()
> Session info -----------------------------------------------------------------------------------------------------------
> setting value
> version R version 3.3.1 (2016-06-21)
> system x86_64, darwin13.4.0
> ui X11
> language (EN)
> collate en_US.UTF-8
> tz America/New_York
> date 2016-09-08
>
> Packages ---------------------------------------------------------------------------------------------------------------
> package * version date source
> BiocGenerics * 0.18.0 2016-05-04 Bioconductor
> colorout * 1.1-2 2016-05-05 Github (jalvesaq/colorout at 6538970)
> devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
> digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
> GenomeInfoDb * 1.8.3 2016-07-13 Bioconductor
> GenomicRanges * 1.24.2 2016-06-15 Bioconductor
> IRanges * 2.6.1 2016-06-19 Bioconductor
> memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
> S4Vectors * 0.10.2 2016-07-08 Bioconductor
> withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
> XVector 0.12.0 2016-05-04 Bioconductor
> zlibbioc 1.18.0 2016-05-04 Bioconductor
>>
>
> Bioc-devel info:
>
>> library(GenomicRanges)
> Loading required package: stats4
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
> duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
> is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
> paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
> Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unsplit, which, which.max, which.min
>
> Loading required package: S4Vectors
>
> Attaching package: ‘S4Vectors’
>
> The following objects are masked from ‘package:base’:
>
> colMeans, colSums, expand.grid, rowMeans, rowSums
>
> Loading required package: IRanges
> Loading required package: GenomeInfoDb
>> l <- CharacterList(list(NA, NA, '1', '2'))
>> r <- CharacterList(as.list(letters[1:4]))
>> tmp <- merge(l, r, all = TRUE)
> Error in V_recycle(value, x, x_what = "value", skeleton_what = "x") :
> 'NROW(value)' is 0 but 'length(x)' is not
> In addition: Warning messages:
> 1: In if (any(duplicated(object))) warning(wmsg("Some of the objects
> to merge contain ", :
> the condition has length > 1 and only the first element will be used
> 2: In if (any(duplicated(object))) warning(wmsg("Some of the objects
> to merge contain ", :
> the condition has length > 1 and only the first element will be used
>> options(width = 120); devtools::session_info()
> Session info -----------------------------------------------------------------------------------------------------------
> setting value
> version R version 3.3.1 (2016-06-21)
> system x86_64, darwin13.4.0
> ui X11
> language (EN)
> collate en_US.UTF-8
> tz America/New_York
> date 2016-09-08
>
> Packages ---------------------------------------------------------------------------------------------------------------
> package * version date source
> BiocGenerics * 0.19.2 2016-07-08 Bioconductor
> colorout * 1.1-2 2016-05-05 Github (jalvesaq/colorout at 6538970)
> devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
> digest 0.6.10 2016-08-02 CRAN (R 3.3.0)
> GenomeInfoDb * 1.9.8 2016-09-04 Bioconductor
> GenomicRanges * 1.25.93 2016-07-28 Bioconductor
> IRanges * 2.7.15 2016-09-04 Bioconductor
> memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
> S4Vectors * 0.11.13 2016-08-16 Bioconductor
> withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
> XVector 0.13.7 2016-07-24 Bioconductor
> zlibbioc 1.19.0 2016-05-05 Bioconductor
>>
>
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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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