[Bioc-sig-seq] ShortRead qa() no longer working

Dario Strbenac D.Strbenac at garvan.org.au
Wed Aug 25 09:00:14 CEST 2010


I've updated my ShortRead and IRanges packages recently and the qa function doesn't work for me anymore. It spends a couple of minutes processing, then fails with an error :

> str(path)
chr "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1"

> dir(path)
[1] "12627LN-FFPET_MBD2IP_1.Rdata"    "12627LN-FFPET_MBD2IP_1.wig.gz"   "12627LN-FFPET_MBD2IP_1_GR.Rdata" "mapping.log"                     "s_1_sequence.fastq.gz"           "s_1_sequence.uniq.map.gz" 

> QAfastq <- qa(path, "fastq.gz", "fastq")
Error in stop(msg, " ", errors, domain = NA) : 
  no function to return from, jumping to top level
Error in slot(object, ".srlist") : 
  cannot get a slot (".srlist") from an object of type "NULL"
In addition: Warning message:
  elements: 1
  UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
 error in evaluating the argument 'dirPath' in selecting a method for function 'qa'

> sessionInfo()
R version 2.11.0 (2010-04-22) 

[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.0     lattice_0.18-5      Biostrings_2.16.0   GenomicRanges_1.0.7 IRanges_1.6.15     

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0

Could this be a bug in the function ?

Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

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