[Bioc-devel] flowCore 1.22.0 broken for some FCS files (which it previously read without errors)

[Kieran O'Neill]

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