[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges
Hervé Pagès
hpages at fredhutch.org
Wed Oct 21 20:14:07 CEST 2015
Hi Michael,
On 10/21/2015 07:09 AM, Michael Lawrence wrote:
> 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?
There was some discussion about this here:
https://support.bioconductor.org/p/70871/
I should probably have brought this to bioc-devel before making that
change, sorry. I'll be happy to bring these methods back if there is a
way to preserve the semantic of base::ifelse() (which relies on delayed
evaluation of the 'yes' and 'no' arguments).
H.
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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