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

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