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

[Michael Lawrence]

News to me. Why was this deprecated? Why can't the ifelse() method just do
what it is now telling the user to do? Is it to make the inefficiency of
the implementation more obvious? The goal with Rle was to make it behave as
conveniently and as vector-like as possible.



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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