The 'GroupedIRanges' error is related to some cleanup Herve is doing on
the subsetting code in IRanges/XVector. The error should be gone with
the most recent devel versions (IRanges 1.19.33, XVector 0.1.2,
GenomicRanges 1.13.42). These may take a day to propagate through
biocLite().
Valerie
On 09/12/2013 08:06 AM, Kasper Daniel Hansen wrote:
We are getting hit hard by this in minfi as well, assuming this is fall out
from us using SummarizedExperiment.
Best,
Kasper
On Thu, Sep 12, 2013 at 7:16 AM, Stadler, Michael <michael.stad...@fmi.ch>wrote:
Dear list and ShortRead maintainers,
Since I updated BioC 2.13 yesterday to the latest package versions, I am
experiencing errors when trying to build the QuasR vignette.
It seems the error is caused in QuasR::preprocessReads(), which tries to
subset a ShortRead::ShortReadQ object with a logical vector.
The problem does not seem to be QuasR related and can be reproduced with a
minimal example:
library(ShortRead)
seqFile <- tempfile(fileext=".fq")
writeLines(c("@seq1/1","AAAGGCCACACTTTTGAAAAAAGAAAAACAAGAATAAGCCCTGTTGCTCT","+","ggggggggggggggggggfffffffffggggggggggggggggggggggg",
"@seq2/1","CTGCCGTAATATTCAGCTCCCTGAGCTGAGCCTTGAGGTCCGAGTTCATC","+","ghgggggggggggggggggfgggfggggggggggggfggggggggggggg",
"@seq3/1","GTTCCACATTGTTCTGCTGTGCTTTGTCCAAATGAACCTTTATGAGCCGG","+","gggggggggggggggggggggggggggggggggggggggggggggggggg",
"@seq4/1","CGGGAGATTCACCAGGACTGGGCTGACCAGGAGTACATTGAGATAATCAC","+","eggegddceedggggeZcec^]`^`ffffcTTSUTTSSTTfffaf]``]^"),
seqFile)
fs1 <- FastqStreamer(seqFile)
chunks <- yield(fs1)
chunks[c(T,F,T,F)] # ERROR
chunks[1:2] # ERROR
close(fs1)
The error message is:
Error in validObject(.Object) :
invalid class “GroupedIRanges” object: slot "group" slot must have same
length as object
My environment is:
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ShortRead_1.19.10 latticeExtra_0.6-26 RColorBrewer_1.0-5
[4] Rsamtools_1.13.39 lattice_0.20-23 Biostrings_2.29.16
[7] GenomicRanges_1.13.41 XVector_0.1.1 IRanges_1.19.32
[10] BiocGenerics_0.7.5
loaded via a namespace (and not attached):
[1] Biobase_2.21.7 bitops_1.0-6 grid_3.0.1 hwriter_1.3
stats4_3.0.1
[6] tools_3.0.1 zlibbioc_1.7.0
Any help would be highly appreciated.
Michael
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