hi,
one of the recent changes in the devel IRanges has been to defunct the
'ifelse' method for 'Rle' objects. This was warned during the previous
devel cycle and so it does with current release.
One of the affected functions is the VRanges object constructor,
'VRanges()'. Since I use this function within my package VariantFiltering,
this is now precluding it to build.
I would like to ask whether you could fix the VRanges constructor to
comply with the new requirement on the 'ifelse' method for 'Rle' objects.
please find below a reproducible example for release and devel with
corresponding session information.
thanks!!
robert.
============================================
This is what happens in current release:
library(VariantAnnotation)
VRanges()
VRanges object with 0 ranges and 0 metadata columns:
seqnames ranges strand ref alt totalDepth
refDepth altDepth sampleNames softFilterMatrix
<Rle> <IRanges> <Rle> <character> <characterOrRle> <integerOrRle>
<integerOrRle> <integerOrRle> <factorOrRle> <matrix>
-------
seqinfo: no sequences
hardFilters: NULL
Warning messages:
1: The "ifelse" methods for Rle objects are deprecated. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
2: The "ifelse" methods for Rle objects are deprecated. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
[6] LC_MESSAGES=en_US.UTF8 LC_PAPER=en_US.UTF8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] VariantAnnotation_1.16.0 Rsamtools_1.22.0 Biostrings_2.38.0
XVector_0.10.0 SummarizedExperiment_1.0.0
[6] Biobase_2.30.0 GenomicRanges_1.22.0 GenomeInfoDb_1.6.0
IRanges_2.4.0 S4Vectors_0.8.0
[11] BiocGenerics_0.16.0 vimcom_1.2-3 setwidth_1.0-4
colorout_1.1-0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.32.0 GenomicAlignments_1.6.0 zlibbioc_1.16.0
BiocParallel_1.4.0 BSgenome_1.38.0 tools_3.2.2
[7] DBI_0.3.1 lambda.r_1.1.7 futile.logger_1.4.1
rtracklayer_1.30.0 futile.options_1.0.0 bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.26.0 RSQLite_1.0.0
GenomicFeatures_1.22.0 XML_3.98-1.3
This is what happens in current devel:
library(VariantAnnotation)
VRanges()
Error: The "ifelse" methods for Rle objects are defunct. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
sessionInfo()
R Under development (unstable) (2015-10-14 r69514)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
[4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] VariantAnnotation_1.17.0 Rsamtools_1.23.0 Biostrings_2.39.0
[4] XVector_0.11.0 SummarizedExperiment_1.1.0 Biobase_2.31.0
[7] GenomicRanges_1.21.32 GenomeInfoDb_1.7.0 IRanges_2.5.1
[10] S4Vectors_0.9.2 BiocGenerics_0.17.0 vimcom_1.0-0
[13] setwidth_1.0-4 colorout_1.0-3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.33.0 GenomicAlignments_1.7.0 zlibbioc_1.17.0
BiocParallel_1.5.0
[5] BSgenome_1.39.0 tools_3.3.0 DBI_0.3.1
lambda.r_1.1.7
[9] futile.logger_1.4.1 rtracklayer_1.31.0 futile.options_1.0.0
bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.27.0 RSQLite_1.0.0
GenomicFeatures_1.23.3
[17] XML_3.98-1.3