[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

[Michael Lawrence]

Just for the record, I've removed the usage of ifelse() by VRanges in
release and devel.

On Wed, Oct 21, 2015 at 6:50 AM, Robert Castelo <robert.castelo at upf.edu>
wrote:

> 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
>
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