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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