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.cast...@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel