[BioC] Problem writing large FCS files using write.FCS in flowCore 1.12.0

[Nishant Gopalakrishnan]

Hi Rob,

Thank as lot for reporting this issue. I was able to reproduce the error
by creating a large flowFrame and trying to write it to an FCS file.

I have checked in a fix for this issue in flowCore version 1.13.10. and
should be available in a day or so via
biocLite().

Nishant

On 04/13/2010 06:34 PM, Robert Bruggner wrote:
> Hi all, 
>
> I'm running flowCore 1.12.0 and am having trouble writing a large FCS file (1.15 million events, 39 channels) using write.FCS(). The error I am getting is:
>
> Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument
>
> For example:
>
>   
>> a = read.FCS(filename="/Users/rbruggner/Desktop/big.fcs")
>> dim(exprs(a))
>>     
> [1] 1143353      39
>   
>> write.FCS(a,filename="/tmp/big.fcs")
>>     
> Error in rep(" ", 8 - nchar(i)) : invalid 'times' argument
>   
>>     
> If I create a new flowFrame with a subset of the events (say, 100k events), the write works correctly. Does anyone have any suggestions as to what might be causing this error?  Many thanks for any suggestions. 
>
> -Rob
>
> Attached session info:
> R version 2.10.1 (2009-12-14) 
> x86_64-apple-darwin9.8.0 
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] flowCore_1.12.0    rrcov_1.0-00       pcaPP_1.8          mvtnorm_0.9-9      robustbase_0.5-0-1 Biobase_2.6.1     
>
> loaded via a namespace (and not attached):
> [1] feature_1.2.4 graph_1.24.1  ks_1.6.8      MASS_7.3-5    stats4_2.10.1 tools_2.10.1 
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