[Bioc-devel] error in subsetting "ShortReadQ" object

[Stadler, Michael]

Thanks Valerie and Herve for the fast fix - I can confirm that the problem is gone with the versions below.
Michael


On Sep 12, 2013, at 11:50 AM, Valerie Obenchain <vobencha at fhcrc.org>
 wrote:

> 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.Stadler at 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
>>> 
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
>> 
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