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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel