[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
Leonardo Collado Torres
|co||@dotor @end|ng |rom gm@||@com
Thu Aug 22 16:50:08 CEST 2019
Hi Michael,
That was using rtracklayer 1.45.3. However I see at
https://github.com/lawremi/rtracklayer/commit/90d4209eae05ae2a4af550072c35cada662b4c89
that you made a recent change. If I use the GitHub version, it all
works =)
> result <- rtracklayer::import(sampleFile,
+ selection = regs,
+ as = 'RleList'
+ )
> result2 <- rtracklayer::import(sampleFile,
+ selection = GenomicRanges::reduce(regs),
+ as = 'RleList'
+ )
> identical(result, result2)
[1] TRUE
library('sessioninfo')
options(width = 120)
session_info()
## Same as yesterday except:
rtracklayer 1.45.3 2019-08-22 [1] Github
(lawremi/rtracklayer using 2dac472)
Best,
Leo
On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence
<lawrence.michael using gene.com> wrote:
>
> 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
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> 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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