Just to follow up on this, I tried flowCore 1.22.3 today, and it worked
perfectly.

Thank-you for the timeous bugfix.

On 13 July 2012 02:51, Cameron Mackenzie <Cameron@luxassure.com> wrote:

> Thank you all very much for addressing our problem so quickly.
> I can send on some error reports and test files but it seems that you
> are already aware of the issues and working on a fix so I propose
> testing the new version when it appears, and getting back in touch if we
> are still having problems.
>
> Cameron
>
>
>
> -----Original Message-----
> From: Finak, Greg [mailto:gfinak@fhcrc.org]
> Sent: 13 July 2012 02:04
> To: Kieran O'Neill
> Cc: Mike; David Corne; Cameron Mackenzie; bioconductor@r-project.org;
> Gottardo, Raphael; Josef Spidlen
> Subject: Re: [BioC] problems reading fcs files / flowcore / read.fcs
> (David Corne)
>
> Kieran,
> Since it's a bug fix it should get pushed to the main page in the next
> day or two.
>
> Greg Finak, PhD
> Staff Scientist
> Vaccine and Infectious Disease Division
> Fred Hutchinson Cancer Research Center
> Seattle, WA
> gfinak@fhcrc.org
> (206) 667-3116
>
> On 2012-07-12, at 5:57 PM, "Kieran O'Neill" <koneill@bccrc.ca> wrote:
>
> > Thanks Mike. That sounds like a good solution.
> >
> > Do you have an idea when 1.22.2 will be released?
> >
> > Thanks,
> > Kieran
> >
> > On 12 July 2012 16:21, Mike <wjiang2@fhcrc.org> wrote:
> >> Hi,All,
> >>
> >> The old version of flowCore didn't take care of double delimiters,
> >> which was valid according to FCS3.0 standard. So we added the patch
> >> to support that. Unfortunately this patch assumed the empty value was
>
> >> not valid for keyword.(since it will be hard to tell the difference
> >> between one pair of single delimiters with empty value and one
> >> double-delimiter)
> >>
> >> In order to still support the FCS generated by some instruments which
>
> >> contains empty values , I've added the argument 'emptyValue' to
> >> read.FCS routine.
> >> Default is TRUE, which automatically excludes the possibility of
> >> double delimiters(they are treated as a pair of start and end single
> >> delimiter with an empty value) Otherwise,empty value are not allowed
> >> and double delimiters are parsed as regular character which is part
> >> of value/keyword string.
> >>
> >> The fix will appear in flowCore version 1.22.2.  Let me know if the
> >> fix solve the problem.
> >> Thanks,
> >>
> >> Mike
> >>
> >> On 07/12/2012 08:08 AM, Finak, Greg wrote:
> >>> Thanks, David and Cameron
> >>> I've added Mike Jiang to the CC list, he's the point person on
> flowCore that will work on fixes.
> >>>
> >>> Best,
> >>>
> >>> Greg Finak, PhD
> >>> Staff Scientist
> >>> Vaccine and Infectious Disease Division Fred Hutchinson Cancer
> >>> Research Center Seattle, WA gfinak@fhcrc.org
> >>> (206) 667-3116
> >>>
> >>> On 2012-07-12, at 7:55 AM, "David Corne" <dwcorne@gmail.com> wrote:
> >>>
> >>>> Dear Greg,
> >>>>
> >>>> Many thanks for that.  I cc Cameron Mackenzie, who is at the
> >>>> coalface trying to deal with this problem.  Yes we expected that
> >>>> this was nonconformist files.
> >>>>
> >>>> Cameron, for specific examples of the most urgent FCS files that
> >>>> you would want to work with PC and the latest R,  I think the thing
>
> >>>> to do is send the error report, and an associated file if possible
> >>>> (e.g. maybe 0ppm?) direct to Greg, and see if his team can fit that
>
> >>>> in.
> >>>>
> >>>> VBD
> >>>>
> >>>> On 12 July 2012 15:45, Finak, Greg <gfinak@fhcrc.org> wrote:
> >>>>> Hi, David
> >>>>> In 2.15 there were some changes to the FCS file reading routine to
> make it compliant with the FCS file standards (it was not compliant
> prior to 2.15, and led to other errors). Unforunately, the result was
> that FCS reading was broken (inadvertently) for files from instruments
> where the manufacturers were not following the standard (apparently
> there are a lot of manufacturers that don't bother to implement the
> standard correctly). We're working on correcting these errors as we get
> bug reports.
> >>>>>
> >>>>> That said, it's next to impossible to help you out if you don't
> provide us with some more information.. i.e. provide a reproducible
> example,  sessioninfo(), the error message produced, and even an example
> of an FCS file where read.FCS fails.
> >>>>>
> >>>>> We want to fix these issues for users, and we understand that
> having software suddenly break when it was fine one version ago can be
> frustrating, but complaining into thin air is not really productive for
> anyone.
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Greg Finak, PhD
> >>>>> Staff Scientist
> >>>>> Vaccine and Infectious Disease Division Fred Hutchinson Cancer
> >>>>> Research Center Seattle, WA gfinak@fhcrc.org
> >>>>> (206) 667-3116
> >>>>>
> >>>>>> ------------------------------
> >>>>>>
> >>>>>> Message: 4
> >>>>>> Date: Wed, 11 Jul 2012 11:58:27 +0100
> >>>>>> From: David Corne <dwcorne@gmail.com>
> >>>>>> To: bioconductor@r-project.org
> >>>>>> Subject: [BioC] problems reading fcs files / flowcore / read.fcs
> >>>>>> Message-ID:
> >>>>>>
> >>>>>> <CAFeka--GMXhzPib9SNWs1oFazAZrvtRSazwPtirTQsVuwnz79g@mail.gmail.c
> >>>>>> om>
> >>>>>> Content-Type: text/plain; charset=ISO-8859-1
> >>>>>>
> >>>>>> Dears All,
> >>>>>>
> >>>>>> I find issues with being able to read FCS files using read.fcs
> >>>>>> from the flowcore package;
> >>>>>>
> >>>>>> So far it seems  FCS files from some instruments can't be read in
>
> >>>>>> R v
> >>>>>> 2.150 on either linux or windows, but with R V 2.13.0  and 2.14.0
>
> >>>>>> they can be read in fine.
> >>>>>>
> >>>>>> It would be nice to be able to use the latest version of R - does
>
> >>>>>> anyone have a fix? Could the flowcore authors maybe release a new
>
> >>>>>> version where read.fcs works in R 2.15.0 ?
> >>>>>>
> >>>>>> VBD
> >>>>> _______________________________________________
> >>>>> Bioconductor mailing list
> >>>>> Bioconductor@r-project.org
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>> Search the archives:
> >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>
> >>>>
> >>>> --
> >>>> -------------------------------------------------------------------
> >>>> -------------------
> >>>> twitter: @dwcorne  / quote: "lightning, striking a cup of tea"
> >>>> -------------------------------------------------------------------
> >>>> -------------------
> >>
> >>
>

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