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#15 MSData.cpp: Detector 0 is out of range; only found 0 detectors

v1.0_(example)
open
nobody
None
5
2017-08-05
2017-08-02
Steffen Neumann
No

Hi, we are hunting down an issue
https://github.com/sneumann/mzR/issues/113
where we have an mzML file that has an instrumentConfiguration with a cvTerm
describing the model, but no componentList inside. It seems (sorry, my C++ is rusty)
that MSData is assuming the presence of componentList, and searching for a detector
throws the error "Detector 0 is out of range; only found 0 detectors".

Are we using pwiz in the wrong way ?

Discussion

  • Brian Pratt

    Brian Pratt - 2017-08-04

    Hi Steffan,

    Could I see the file in question? Legal syntax or not, if it's seen in the
    wild it's best to deal with it gracefully.

    Thanks

    Brian Pratt

    On Wed, Aug 2, 2017 at 1:50 AM, Steffen Neumann sneumann@users.sf.net
    wrote:

    Status: open
    Group: v1.0_(example)
    Created: Wed Aug 02, 2017 08:50 AM UTC by Steffen Neumann
    Last Updated: Wed Aug 02, 2017 08:50 AM UTC
    Owner: nobody

    Hi, we are hunting down an issue
    https://github.com/sneumann/mzR/issues/113
    where we have an mzML file that has an instrumentConfiguration with a
    cvTerm
    describing the model, but no componentList inside. It seems (sorry, my C++
    is rusty)
    that MSData is assuming the presence of componentList, and searching for a
    detector
    throws the error "Detector 0 is out of range; only found 0 detectors".

    Are we using pwiz in the wrong way ?

    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/proteowizard/bugs/15/

    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/

     
    alternate

  • Steffen Neumann

    Steffen Neumann - 2017-08-05

    Hi, here is a file with the same structure as the original culprit,
    also linked in https://github.com/sneumann/mzR/issues/113#issuecomment-319610207
    If you need the original Waters file with the same issue, please contact
    @nsadawi on github. Yours, Steffen

     
    MM14-withoutComponentList.zip

    • Brian Pratt

      Brian Pratt - 2017-08-07

      OK, as you have noted, the problem is in LegacyAdapter, which doesn't get a
      lot of attention around here being, well, legacy. Sounds like you've
      already worked around it on your side, but it should be fixed now in
      Proteowizard as well, and any requests through LegacyAdapter for info from
      a missing ComponentList will come back with "Unknown".

      It looks like you're using a cached copy of the pwiz code, so don't forget
      to update that.

      Thanks for alerting us to the problem!

      Brian

      On Sat, Aug 5, 2017 at 4:47 AM, Steffen Neumann sneumann@users.sf.net
      wrote:

      Hi, here is a file with the same structure as the original culprit,
      also linked in https://github.com/sneumann/mzR/issues/113#issuecomment-
      319610207
      If you need the original Waters file with the same issue, please contact
      @nsadawi on github. Yours, Steffen

      Attachments:

      Status: open
      Group: v1.0_(example)
      Created: Wed Aug 02, 2017 08:50 AM UTC by Steffen Neumann
      Last Updated: Wed Aug 02, 2017 08:50 AM UTC
      Owner: nobody

      Hi, we are hunting down an issue
      https://github.com/sneumann/mzR/issues/113
      where we have an mzML file that has an instrumentConfiguration with a
      cvTerm
      describing the model, but no componentList inside. It seems (sorry, my C++
      is rusty)
      that MSData is assuming the presence of componentList, and searching for a
      detector
      throws the error "Detector 0 is out of range; only found 0 detectors".

      Are we using pwiz in the wrong way ?

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/proteowizard/bugs/15/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

       

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