Thanks Hervé for fixing this!
Best,
Leo
On Sat, Sep 10, 2016 at 5:47 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> 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@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@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
>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> 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: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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