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

[Robert Castelo]

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