Entering edit mode
Hello,
I'm having a strange issue in R 3.5.0 / Bioc 3.7 when trying to assign seqinfo to a bsseq object that I don't have in R 3.4.3 / Bioc 3.6. The particular error I get can be reproduced with the following code:
# Do not load any libraries
seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19')
M <- matrix(0:8, 3, 3)
Cov <- matrix(1:9, 3, 3)
bs <- bsseq::BSseq(chr = c("chr1", "chr2", "chr1"), pos = c(1,2,3),
M = M, Cov = Cov, sampleNames = c("A","B","C"))
GenomeInfoDb::seqinfo(bs) = seqinfo_hg19[GenomeInfoDb::seqlevelsInUse(bs)]
And the last line produces the error:
Error in methods::slot(object, name) :
no slot of name "call" for this object of class "GRanges"
I have boiled it down to the following toy examples, tested on R 3.5.0 / Bioc 3.7 with the Bioc docker images, and R 3.4.z / Bioc 3.6 locally / on some servers at work (session infos at the end). The 1B and 2B blocks below are closer to the style in which I'm actually calling these functions from within a package that imports GenomicRanges, GenomeInfoDb, and bsseq, among other packages.
# Run each in different R sessions
################################################################################
# BLOCK 1A
# WORKS in R 3.4.z / Bioc 3.6 and WORKS in R 3.5.0 / Bioc 3.7
library(GenomicRanges)
seqinfo_hg19 = Seqinfo(genome = 'hg19')
gr <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
IRanges(1:10, width=10:1))
seqlevelsInUse(gr)
seqinfo(gr) = seqinfo_hg19[seqlevelsInUse(gr)]
################################################################################
# BLOCK 1B
# WORKS in R 3.4.z / Bioc 3.6 and WORKS in R 3.5.0 / Bioc 3.7
seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19')
gr <- GenomicRanges::GRanges(S4Vectors::Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
IRanges::IRanges(1:10, width=10:1))
GenomeInfoDb::seqlevelsInUse(gr)
GenomeInfoDb::seqinfo(gr) = seqinfo_hg19[GenomeInfoDb::seqlevelsInUse(gr)]
################################################################################
# BLOCK 2A
# WORKS in R 3.4.z / Bioc 3.6 and WORKS in R 3.5.0 / Bioc 3.7
library(bsseq)
seqinfo_hg19 = Seqinfo(genome = 'hg19')
M <- matrix(0:8, 3, 3)
Cov <- matrix(1:9, 3, 3)
bs <- BSseq(chr = c("chr1", "chr2", "chr1"), pos = c(1,2,3),
M = M, Cov = Cov, sampleNames = c("A","B","C"))
seqinfo(bs) = seqinfo_hg19[seqlevelsInUse(bs)]
################################################################################
# BLOCK 2B
# WORKS in R 3.4.z / Bioc 3.6 and FAILS in R 3.5.0 / Bioc 3.7
seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19')
M <- matrix(0:8, 3, 3)
Cov <- matrix(1:9, 3, 3)
bs <- bsseq::BSseq(chr = c("chr1", "chr2", "chr1"), pos = c(1,2,3),
M = M, Cov = Cov, sampleNames = c("A","B","C"))
GenomeInfoDb::seqinfo(bs) = seqinfo_hg19[GenomeInfoDb::seqlevelsInUse(bs)]
The fact that blocks 1A and 1B don't fail indicates that the issue is in bsseq, and not GenomicRanges. Also, calling library(bsseq) appears to change the NAMESPACE in such a way that the error isn't produced in R 3.5.0 / Bioc 3.7. Since the code being executed is within a package, the best I can do is import the package, and not use library(bsseq).
Any insight into what might be causing this would greatly be appreciated. I'm rather stumped.
Below is the session info for R 3.4.3 / Bioc 3.6:
Session info ------------------------------------------------------------------
setting value
version R version 3.4.3 (2017-11-30)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz <NA>
date 2018-05-14
Packages ----------------------------------------------------------------------
package * version date source
base * 3.4.3 2018-02-25 local
Biobase 2.38.0 2018-04-11 Bioconductor
BiocGenerics 0.24.0 2018-04-11 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.4.3)
bsseq 1.14.0 2018-04-11 Bioconductor
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.3)
compiler 3.4.3 2018-02-25 local
data.table 1.10.4-3 2017-10-27 CRAN (R 3.4.3)
datasets * 3.4.3 2018-02-25 local
DelayedArray 0.4.1 2018-04-11 Bioconductor
devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
GenomeInfoDb 1.14.1 2018-04-11 Bioconductor
GenomeInfoDbData 1.0.0 2018-04-11 Bioconductor
GenomicRanges 1.30.3 2018-04-11 Bioconductor
graphics * 3.4.3 2018-02-25 local
grDevices * 3.4.3 2018-02-25 local
grid 3.4.3 2018-02-25 local
gtools 3.5.0 2015-05-29 CRAN (R 3.4.3)
IRanges 2.12.0 2018-04-11 Bioconductor
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
limma 3.34.9 2018-04-11 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.4.3)
Matrix 1.2-14 2018-04-09 CRAN (R 3.4.3)
matrixStats 0.53.1 2018-02-11 CRAN (R 3.4.3)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.3)
methods * 3.4.3 2018-02-25 local
munsell 0.4.3 2016-02-13 CRAN (R 3.4.3)
packrat 0.4.9-1 2018-03-12 CRAN (R 3.4.3)
parallel 3.4.3 2018-02-25 local
permute 0.9-4 2016-09-09 CRAN (R 3.4.3)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.3)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.4.3)
R.oo 1.21.0 2016-11-01 CRAN (R 3.4.3)
R.utils 2.6.0 2017-11-05 CRAN (R 3.4.3)
Rcpp 0.12.16 2018-03-13 CRAN (R 3.4.3)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.4.3)
S4Vectors 0.16.0 2018-04-11 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.4.3)
stats * 3.4.3 2018-02-25 local
stats4 3.4.3 2018-02-25 local
SummarizedExperiment 1.8.1 2018-04-11 Bioconductor
tools 3.4.3 2018-02-25 local
utils * 3.4.3 2018-02-25 local
withr 2.1.2 2018-03-15 CRAN (R 3.4.3)
XVector 0.18.0 2018-04-11 Bioconductor
zlibbioc 1.24.0 2018-04-11 Bioconductor
And below is for R 3.5.0 / Bioc 3.7:
Session info ------------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz Etc/UTC
date 2018-05-14
Packages ----------------------------------------------------------------------
package * version date source
base * 3.5.0 2018-05-01 local
Biobase 2.40.0 2018-05-08 Bioconductor
BiocGenerics 0.26.0 2018-05-08 Bioconductor
BiocInstaller * 1.30.0 2018-05-08 Bioconductor
BiocParallel 1.14.1 2018-05-08 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.5.0)
bsseq 1.16.0 2018-05-11 Bioconductor
colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
compiler 3.5.0 2018-05-01 local
data.table 1.11.2 2018-05-08 CRAN (R 3.5.0)
datasets * 3.5.0 2018-05-01 local
DelayedArray 0.6.0 2018-05-11 Bioconductor
DelayedMatrixStats 1.2.0 2018-05-11 Bioconductor
devtools 1.13.5 2018-02-18 CRAN (R 3.5.0)
digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
GenomeInfoDb 1.16.0 2018-05-08 Bioconductor
GenomeInfoDbData 1.1.0 2018-05-08 Bioconductor
GenomicRanges 1.32.2 2018-05-08 Bioconductor
graphics * 3.5.0 2018-05-01 local
grDevices * 3.5.0 2018-05-01 local
grid 3.5.0 2018-05-01 local
gtools 3.5.0 2015-05-29 CRAN (R 3.5.0)
HDF5Array 1.8.0 2018-05-11 Bioconductor
IRanges 2.14.8 2018-05-14 Bioconductor
lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
limma 3.36.1 2018-05-11 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.5.0)
Matrix 1.2-14 2018-04-09 CRAN (R 3.5.0)
matrixStats 0.53.1 2018-02-11 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.0 2018-05-01 local
munsell 0.4.3 2016-02-13 CRAN (R 3.5.0)
parallel 3.5.0 2018-05-01 local
permute 0.9-4 2016-09-09 CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.5.0)
R.oo 1.22.0 2018-04-22 CRAN (R 3.5.0)
R.utils 2.6.0 2017-11-05 CRAN (R 3.5.0)
Rcpp 0.12.16 2018-03-13 CRAN (R 3.5.0)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.5.0)
rhdf5 2.24.0 2018-05-11 Bioconductor
Rhdf5lib 1.2.0 2018-05-11 Bioconductor
S4Vectors 0.18.1 2018-05-08 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.5.0)
stats * 3.5.0 2018-05-01 local
stats4 3.5.0 2018-05-01 local
SummarizedExperiment 1.10.1 2018-05-11 Bioconductor
tools 3.5.0 2018-05-01 local
utils * 3.5.0 2018-05-01 local
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
XVector 0.20.0 2018-05-08 Bioconductor
zlibbioc 1.26.0 2018-05-08 Bioconductor
Thanks for the detailed bug report, @rcavalca. I can confirm that running 2B in a clean session leads to the error. However, it's not an issue with bsseq but rather something else, perhaps in SummarizedExpeirment. On BioC 3.7:
Created on 2018-05-14 by the reprex package (v0.2.0).
Hopefully Hervé Pagès can chime in. It's a little unusual to use these packages in a script without first calling
library()but you mention you encountered this issue in a package. Are you able to link to it (a GitHub repo, for example)?Posted this as a GitHub issue.