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

Robert Bruggner bruggner at stanford.edu
Wed Apr 14 03:34:53 CEST 2010

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. 


Attached session info:
R version 2.10.1 (2009-12-14) 

[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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