[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
Sat Aug 24 20:48:35 CEST 2019


Sorry about that. I bumped the version and ported to release.

On Thu, Aug 22, 2019 at 7:50 AM Leonardo Collado Torres
<lcolladotor using gmail.com> wrote:
>
> 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
> >
> > Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube



-- 
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube



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