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 <lcollado...@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@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@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 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
