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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
>> 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
