Kieran,

I looked at your FCS, it has empty keyword value which does not conform to FCS 3.0 standard:
"3.2.9 Keywords and keyword values must have lengths greater than zero. "(http://murphylab.cbi.cmu.edu/FCSAPI/FCS3.html).

Particularly, this occurs at $ENDSTEXT keyword-value pairs :"\\$ENDSTEXT\\\\$ETIM..."
Which is "byte offset to end of the supplemental TEXT segment" and really shouldn't be empty (normally it is put as "0")

And "\\" is used as delimiter here, FCS 3.0 allows delimiter appears in the keyword value or keyword name as long as it is " immediately followed by a second delimiter". So the characters "\\\\" after "$ENDSTEXT" keyword is misunderstood as part of "$ETIM" by the parser here, which further messed up the parsing of subsequent string. That is why the parser is reporting error.

Originally,flowCore did not handle this delimiter issue properly. It might read FCS successfully with the incorrect keyword values without notifying the user. Now,we thought it may be helpful to throw the error and let user know the issue with the TEXT segment of FCS.

I have attached the TEXT Segment of your FCS file.

Let me know if you have questions.

Thanks,
Mike
> From: Kieran O'Neill <koneill@bccrc.ca>
> Subject: [Bioc-devel] flowCore 1.22.0 broken for some FCS files (which it previously read without errors)
> Date: June 13, 2012 3:53:17 PM PDT
> To: bioc-devel@r-project.org
> Hi all
>
> I just recently came back to a project I was previously working on,
> and found that the most recent version of flowCore, 1.22.0, no longer
> reads some of my FCS files (those generated by one instrument in
> particular).
>
> The error it gives is:
>
> Error in fcs_text_parse(txt) : ERROR! no end found
>
> Previous versions of flowCore had no trouble reading these files, and
> the current version seems to read most other FCS files I have from
> other instruments. However, since parsing FCS files into something
> usable in R is probably the most important functionality in the
> package, having it broken is rather bad.
>
> It is also quite frustrating for me, in that no previous version of
> flowCore works in the current version of R (2.15.0), so I would need
> to downgrade the whole of R in order to downgrade to a working version
> of flowCore to analyse these files.
>
> I would be happy to send a sample file for debugging if needed.
>
> Thanks,
> Kieran
>
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