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
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