[BioC] Help with Prada Package: Installation and Run

[Martin Morgan]

Taking a peak at the directory where the files are stored shows

> list.files(system.file('extdata', package='prada'))
...
 [5] "fas-Bcl2-plate323-04-04.A01"             
...

so there are no spaces in the file name, just hyphens.

Martin

Oleg Sklyar <osklyar at ebi.ac.uk> writes:

>>> filepath <- system.file("extdata", "fas Bcl2 plate323 -04-04.A01", package
>> =
>> + "prada")
>>> filepath
>> [1] ""
>>> sampdat <- readFCS(filepath)
>> Error: filename != "" is not TRUE
>
> You did the print for 'filepath' and it shows [1] "", which means that 
> in readFCS you are trying to read a missing file. Thus it is reasonable 
> that you get an error message which checks the condition whether the 
> file name you supplied is not empty. In this case it is, thus the result 
> is not TRUE. There is probably a statement in the code: 
> stopifnot(filename != "") which outputds exactly what you see.
>
> So it probably has nothing to do with installation and rather with the 
> file name supplied in this example. In fact, check the spaces in the 
> file name, maybe they need to be escaped with a \ ?



> Best
> Oleg
>
> -- 
> Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org