[BioC] Cannot call ShortRead package FastqSampler from Linux

talshay talshay at broadinstitute.org
Wed May 30 22:35:44 CEST 2012


I have huge Fastq paired RNA-seq file that I am trying to down-sample.
It seems ShortRead Package 1.6.2 FastqSampler class should do that, but 
I can't call it from Linux.

 > library("ShortRead")
 > f1 <- FastqSampler(file_name, n=50)
Error: could not find function "FastqSampler"
 > getClassDef("FastqSampler")

Session info below shows that the package is loaded - what am I missing 
FastqSampler is documented as a class and not a method, but all samples 
I found seem to be using it the same way, and it is recognized when I do 
the same on my Windows PC.

Thanks for any help,

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

[1] C

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

other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.1     lattice_0.18-5
[4] Biostrings_2.16.9   GenomicRanges_1.0.9 IRanges_1.6.17

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

This seems to be specific to the Linux version, as when I do the same on 
my Windows PC, FastqSampler is recognized.

 > getClassDef("FastqSampler")
Reference Class "FastqSampler":

Class fields:

Name:              con          reader readerBlockSize       
recParser    recSeperator               n         saved_n           
tot_n         records             buf         verbose
Class:             ANY        function         integer        
function             raw         integer         integer         
integer            list             raw         logical

  Class Methods:
     ".add", ".flush", ".getCurrent", ".sampler_msg", "callSuper", 
"export", "get", "import", "initFields", "reset", "sample", "status"

  Reference Superclasses:
     "Sampler", "envRefClass"

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