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
>
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