Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
Sorry about that. I bumped the version and ported to release.
On Thu, Aug 22, 2019 at 7:50 AM Leonardo Collado Torres
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:
> rtracklayer1.45.32019-08-22 [1] Github
> (lawremi/rtracklayer@2dac472)
>
> Best,
> Leo
>
> On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence
> 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
> > 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(
> > > 'SRR38' =
> > > 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.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
> > > # ctypeen_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)
> > > # Biobase2.45.02019-05-02 [1] Bioconductor
> > > # BiocGenerics 0.31.52019-07-03 [1] Bioconductor
> > > # BiocParallel 1.19.22019-08-07 [1] Bioconductor
> > > # Biostrings 2.53.22019-07-09 [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)
> > > # cli1.1.0 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
Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
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:
rtracklayer1.45.32019-08-22 [1] Github
(lawremi/rtracklayer@2dac472)
Best,
Leo
On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence
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
> 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(
> > 'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.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
> > # ctypeen_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)
> > # Biobase2.45.02019-05-02 [1] Bioconductor
> > # BiocGenerics 0.31.52019-07-03 [1] Bioconductor
> > # BiocParallel 1.19.22019-08-07 [1] Bioconductor
> > # Biostrings 2.53.22019-07-09 [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)
> > # cli1.1.0 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 0.11.42019-07-03 [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 0.6.202019-07-04 [1] CRAN (R 3.6.0)
> > # fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
> > # GenomeInfoDb 1.21.12019-05-16 [1]
Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
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
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(
> 'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.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
> # ctypeen_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)
> # Biobase2.45.02019-05-02 [1] Bioconductor
> # BiocGenerics 0.31.52019-07-03 [1] Bioconductor
> # BiocParallel 1.19.22019-08-07 [1] Bioconductor
> # Biostrings 2.53.22019-07-09 [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)
> # cli1.1.0 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 0.11.42019-07-03 [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 0.6.202019-07-04 [1] CRAN (R 3.6.0)
> # fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
> # GenomeInfoDb 1.21.12019-05-16 [1] Bioconductor
> # GenomeInfoDbData 1.2.1 2019-07-27 [1] Bioconductor
> # GenomicAlignments 1.21.42019-06-28 [1] Bioconductor
> # GenomicRanges 1.37.14 2019-06-24 [1] Bioconductor
> # glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
> # IRanges2.19.10 2019-06-11 [1] Bioconductor
> # lattice0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
> # magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
> # Matrix 1.2-172019-03-22 [1] CRAN (R 3.6.1)
> # matrixStats0.54.02018-07-23 [1] CRAN (R 3.6.0)
> # memoise1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
> # pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
> # pkgload1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
> # prettyunits1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
> # processx 3.4.1
[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors
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(
'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.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
# ctypeen_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)
# Biobase2.45.02019-05-02 [1] Bioconductor
# BiocGenerics 0.31.52019-07-03 [1] Bioconductor
# BiocParallel 1.19.22019-08-07 [1] Bioconductor
# Biostrings 2.53.22019-07-09 [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)
# cli1.1.0 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 0.11.42019-07-03 [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 0.6.202019-07-04 [1] CRAN (R 3.6.0)
# fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
# GenomeInfoDb 1.21.12019-05-16 [1] Bioconductor
# GenomeInfoDbData 1.2.1 2019-07-27 [1] Bioconductor
# GenomicAlignments 1.21.42019-06-28 [1] Bioconductor
# GenomicRanges 1.37.14 2019-06-24 [1] Bioconductor
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
# IRanges2.19.10 2019-06-11 [1] Bioconductor
# lattice0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
# Matrix 1.2-172019-03-22 [1] CRAN (R 3.6.1)
# matrixStats0.54.02018-07-23 [1] CRAN (R 3.6.0)
# memoise1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
# pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
# pkgload1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
# prettyunits1.0.2 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)
# remotes2.1.0 2019-06-24 [1] CRAN (R
