[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
Michael Lawrence
|@wrence@m|ch@e| @end|ng |rom gene@com
Wed Aug 21 21:33:35 CEST 2019
Sorry, please try 1.45.3. If that works then I'll push it over to release.
On Wed, Aug 21, 2019 at 11:48 AM Leonardo Collado Torres
<lcolladotor using gmail.com> wrote:
>
> Dear Bioc-devel,
>
> In BioC 3.9 and 3.10 I've noticed some errors on recount which today I
> finally traced. It looks like the internals of
> rtracklayer::import.bw() changed (or mabye S4Vectors:::normarg_names)
> in such a way that if you specify as input to rtracklayer::import()
> the "selection" argument with a named GRanges object that has repeated
> ranges, the function call fails. This can be avoided from a user's
> perspective by using GenomicRanges::reduce() on the input to
> "selection", which I guess is ultimately the best option. I now use
> GenomicRanges::reduce() on derfinder version 1.18.4 (BioC 3.9) and
> 1.19.4 (BioC 3.10) to solve this issue for recount. But well, I
> thought that it would be best to share this with all of you.
>
> Best,
> Leo
>
> Here's the actual R code for reproducing this situation:
>
>
>
> sampleFile <- c(
> 'SRR387777' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
> )
> regs <- GenomicRanges::GRanges(
> 'chrY',
> IRanges::IRanges(start = c(1, 1), width = 10),
> strand = '-'
> )
> names(regs) <- c(1:2)
> result <- rtracklayer::import(sampleFile,
> selection = regs,
> as = 'RleList'
> )
> # Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
> # attempt to set too many names (2) on IRanges object of length 1
>
> # 12: stop(wmsg("attempt to set too many names (", names_len, ") ",
> # "on ", x_class, " object of length ", x_len))
> # 11: S4Vectors:::normarg_names(value, class(x), length(x))
> # 10: `names<-`(`*tmp*`, value = nm)
> # 9: `names<-`(`*tmp*`, value = nm)
> # 8: setNames(ranges(x), value)
> # 7: `names<-`(`*tmp*`, value = names(flatWhich))
> # 6: `names<-`(`*tmp*`, value = names(flatWhich))
> # 5: .local(con, format, text, ...)
> # 4: import(FileForFormat(con), ...)
> # 3: import(FileForFormat(con), ...)
> # 2: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
> # 1: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
>
> result <- rtracklayer::import(sampleFile,
> selection = GenomicRanges::reduce(regs),
> as = 'RleList'
> )
>
> library('sessioninfo')
> options(width = 120)
> session_info()
>
> # ─ Session info
> ───────────────────────────────────────────────────────────────────────────────────────────────────────
> # setting value
> # version R version 3.6.1 (2019-07-05)
> # os macOS Mojave 10.14.6
> # system x86_64, darwin15.6.0
> # ui X11
> # language (EN)
> # collate en_US.UTF-8
> # ctype en_US.UTF-8
> # tz America/New_York
> # date 2019-08-21
> #
> # ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
> # package * version date lib source
> # assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
> # backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
> # Biobase 2.45.0 2019-05-02 [1] Bioconductor
> # BiocGenerics 0.31.5 2019-07-03 [1] Bioconductor
> # BiocParallel 1.19.2 2019-08-07 [1] Bioconductor
> # Biostrings 2.53.2 2019-07-09 [1] Bioconductor
> # bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
> # callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.0)
> # cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
> # colorout * 1.2-1 2019-07-27 [1] Github
> (jalvesaq/colorout using 7ea9440)
> # crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
> # DelayedArray 0.11.4 2019-07-03 [1] Bioconductor
> # desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
> # devtools * 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
> # digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0)
> # fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
> # GenomeInfoDb 1.21.1 2019-05-16 [1] Bioconductor
> # GenomeInfoDbData 1.2.1 2019-07-27 [1] Bioconductor
> # GenomicAlignments 1.21.4 2019-06-28 [1] Bioconductor
> # GenomicRanges 1.37.14 2019-06-24 [1] Bioconductor
> # glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
> # IRanges 2.19.10 2019-06-11 [1] Bioconductor
> # lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
> # magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
> # Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.6.1)
> # matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.6.0)
> # memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
> # pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
> # pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
> # prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
> # processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
> # ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
> # R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
> # Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
> # RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
> # remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
> # rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
> # rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
> # Rsamtools 2.1.3 2019-07-05 [1] Bioconductor
> # rtracklayer 1.45.3 2019-08-16 [1] Bioconductor
> # S4Vectors 0.23.18 2019-08-16 [1] Bioconductor
> # sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
> # SummarizedExperiment 1.15.6 2019-07-31 [1] Bioconductor
> # testthat * 2.2.1 2019-07-25 [1] CRAN (R 3.6.0)
> # usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
> # withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
> # XML 3.98-1.20 2019-06-06 [1] CRAN (R 3.6.0)
> # XVector 0.25.0 2019-05-02 [1] Bioconductor
> # zlibbioc 1.31.0 2019-05-02 [1] Bioconductor
> #
> # [1] /Library/Frameworks/R.framework/Versions/3.6devel/Resources/library
>
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--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com
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