Thread: [proteowizard-support] msconvert : Error writing run 1

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proteowizard-support

[proteowizard-support] msconvert : Error writing run 1

From: Yagnesh U. <yu...@ca...> - 2014-07-15 15:38:42

Hello,

I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.

However, running msconvert gives a "Error writing run 1" message:

wine msconvert.exe DR_band1_280514_run1.RAW

format: mzML
     m/z: Compression-None, 64-bit
     intensity: Compression-None, 32-bit
     rt: Compression-None, 64-bit
ByteOrder_LittleEndian
  indexed="true"
outputPath: .
extension: .mzML
contactFilename:

filters:

filenames:
   DR_band1_280514_run1.RAW

processing file: DR_band1_280514_run1.RAW
fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
Error writing run 1 in "DR_band1_280514_run1.RAW":
boost::interprocess_exception::library_error


Any help would be appreciated!

Many thanks,
Yagnesh

Re: [proteowizard-support] msconvert : Error writing run 1

From: Brian P. <bs...@pr...> - 2014-07-15 16:26:04

These two lines:

fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!

make me think you've hit the limitations of Wine.

Perhaps there's a newer version of Wine that implements these windows API
points.  Please do report back to the list if you succeed!

Brian


On Tue, Jul 15, 2014 at 8:38 AM, Yagnesh Umrania <yu...@ca...> wrote:

> Hello,
>
> I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.
>
> However, running msconvert gives a "Error writing run 1" message:
>
> wine msconvert.exe DR_band1_280514_run1.RAW
>
> format: mzML
>      m/z: Compression-None, 64-bit
>      intensity: Compression-None, 32-bit
>      rt: Compression-None, 64-bit
> ByteOrder_LittleEndian
>   indexed="true"
> outputPath: .
> extension: .mzML
> contactFilename:
>
> filters:
>
> filenames:
>    DR_band1_280514_run1.RAW
>
> processing file: DR_band1_280514_run1.RAW
> fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
> Error writing run 1 in "DR_band1_280514_run1.RAW":
> boost::interprocess_exception::library_error
>
>
> Any help would be appreciated!
>
> Many thanks,
> Yagnesh
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>

Re: [proteowizard-support] msconvert : Error writing run 1

From: Chambers, M. <mat...@gm...> - 2014-07-15 16:29:37

I suspect it's the interprocess_exception that's killing it. I recently 
changed SHA1 calc to use memory mapped files on Windows to support UTF8 
filenames and improve performance. The cross-platform implementation is 
provided by boost::interprocess. It's likely that that implementation is 
breaking down on Wine, although I don't know. Unfortunately, I don't 
really have the bandwidth to support Wine. You can try to get an older 
version of pwiz before the SHA1 change and it may work.

Sorry,
-Matt


On 7/15/2014 10:38 AM, Yagnesh Umrania wrote:
> Hello,
>
> I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.
>
> However, running msconvert gives a "Error writing run 1" message:
>
> wine msconvert.exe DR_band1_280514_run1.RAW
>
> format: mzML
>       m/z: Compression-None, 64-bit
>       intensity: Compression-None, 32-bit
>       rt: Compression-None, 64-bit
> ByteOrder_LittleEndian
>    indexed="true"
> outputPath: .
> extension: .mzML
> contactFilename:
>
> filters:
>
> filenames:
>     DR_band1_280514_run1.RAW
>
> processing file: DR_band1_280514_run1.RAW
> fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
> Error writing run 1 in "DR_band1_280514_run1.RAW":
> boost::interprocess_exception::library_error
>
>
> Any help would be appreciated!
>
> Many thanks,
> Yagnesh
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support

Re: [proteowizard-support] msconvert : Error writing run 1

From: Joseph S. <Jos...@sy...> - 2014-07-21 17:07:14

That's disappointing to hear as many organizations do have significant
Linux compute resources.  I'm sure I'm not alone in wishing the Wine
solution would simplify proteomics analysis pipelines.

-Joe



On Tue, Jul 15, 2014 at 9:29 AM, Chambers, Matthew <
mat...@gm...> wrote:

> I suspect it's the interprocess_exception that's killing it. I recently
> changed SHA1 calc to use memory mapped files on Windows to support UTF8
> filenames and improve performance. The cross-platform implementation is
> provided by boost::interprocess. It's likely that that implementation is
> breaking down on Wine, although I don't know. Unfortunately, I don't
> really have the bandwidth to support Wine. You can try to get an older
> version of pwiz before the SHA1 change and it may work.
>
> Sorry,
> -Matt
>
>
> On 7/15/2014 10:38 AM, Yagnesh Umrania wrote:
> > Hello,
> >
> > I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.
> >
> > However, running msconvert gives a "Error writing run 1" message:
> >
> > wine msconvert.exe DR_band1_280514_run1.RAW
> >
> > format: mzML
> >       m/z: Compression-None, 64-bit
> >       intensity: Compression-None, 32-bit
> >       rt: Compression-None, 64-bit
> > ByteOrder_LittleEndian
> >    indexed="true"
> > outputPath: .
> > extension: .mzML
> > contactFilename:
> >
> > filters:
> >
> > filenames:
> >     DR_band1_280514_run1.RAW
> >
> > processing file: DR_band1_280514_run1.RAW
> > fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> > fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
> > Error writing run 1 in "DR_band1_280514_run1.RAW":
> > boost::interprocess_exception::library_error
> >
> >
> > Any help would be appreciated!
> >
> > Many thanks,
> > Yagnesh
> >
> >
> >
> ------------------------------------------------------------------------------
> > Want fast and easy access to all the code in your enterprise? Index and
> > search up to 200,000 lines of code with a free copy of Black Duck
> > Code Sight - the same software that powers the world's largest code
> > search on Ohloh, the Black Duck Open Hub! Try it now.
> > http://p.sf.net/sfu/bds
> > _______________________________________________
> > proteowizard-support mailing list
> > pro...@li...
> > https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>



-- 
Joe Slagel
Institute for Systems Biology
js...@sy...
(206) 732-1362

Re: [proteowizard-support] msconvert : Error writing run 1

From: Chambers, M. <mat...@gm...> - 2014-07-21 18:03:18

I agree. Is there a way to detect that the code is running under Wine 
and I can just branch on that to use the older non-UTF8 code?

-Matt


On 7/21/2014 12:07 PM, Joseph Slagel wrote:
> That's disappointing to hear as many organizations do have significant 
> Linux compute resources.  I'm sure I'm not alone in wishing the Wine 
> solution would simplify proteomics analysis pipelines.
>
> -Joe
>
>
>
> On Tue, Jul 15, 2014 at 9:29 AM, Chambers, Matthew 
> <mat...@gm... <mailto:mat...@gm...>> wrote:
>
>     I suspect it's the interprocess_exception that's killing it. I
>     recently
>     changed SHA1 calc to use memory mapped files on Windows to support
>     UTF8
>     filenames and improve performance. The cross-platform
>     implementation is
>     provided by boost::interprocess. It's likely that that
>     implementation is
>     breaking down on Wine, although I don't know. Unfortunately, I don't
>     really have the bandwidth to support Wine. You can try to get an older
>     version of pwiz before the SHA1 change and it may work.
>
>     Sorry,
>     -Matt
>
>
>     On 7/15/2014 10:38 AM, Yagnesh Umrania wrote:
>     > Hello,
>     >
>     > I am trying to run msconvert in linux (ubuntu 14.04) with wine
>     1.7.22.
>     >
>     > However, running msconvert gives a "Error writing run 1" message:
>     >
>     > wine msconvert.exe DR_band1_280514_run1.RAW
>     >
>     > format: mzML
>     >       m/z: Compression-None, 64-bit
>     >       intensity: Compression-None, 32-bit
>     >       rt: Compression-None, 64-bit
>     > ByteOrder_LittleEndian
>     >    indexed="true"
>     > outputPath: .
>     > extension: .mzML
>     > contactFilename:
>     >
>     > filters:
>     >
>     > filenames:
>     >     DR_band1_280514_run1.RAW
>     >
>     > processing file: DR_band1_280514_run1.RAW
>     > fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
>     > fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
>     > Error writing run 1 in "DR_band1_280514_run1.RAW":
>     > boost::interprocess_exception::library_error
>     >
>     >
>     > Any help would be appreciated!
>     >
>     > Many thanks,
>     > Yagnesh
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Want fast and easy access to all the code in your enterprise?
>     Index and
>     > search up to 200,000 lines of code with a free copy of Black Duck
>     > Code Sight - the same software that powers the world's largest code
>     > search on Ohloh, the Black Duck Open Hub! Try it now.
>     > http://p.sf.net/sfu/bds
>     > _______________________________________________
>     > proteowizard-support mailing list
>     > pro...@li...
>     <mailto:pro...@li...>
>     > https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>
>     ------------------------------------------------------------------------------
>     Want fast and easy access to all the code in your enterprise?
>     Index and
>     search up to 200,000 lines of code with a free copy of Black Duck
>     Code Sight - the same software that powers the world's largest code
>     search on Ohloh, the Black Duck Open Hub! Try it now.
>     http://p.sf.net/sfu/bds
>     _______________________________________________
>     proteowizard-support mailing list
>     pro...@li...
>     <mailto:pro...@li...>
>     https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>
>
>
> -- 
> Joe Slagel
> Institute for Systems Biology
> js...@sy... <mailto:js...@sy...>
> (206) 732-1362

Re: [proteowizard-support] msconvert : Error writing run 1

From: James C. <jca...@sa...> - 2014-10-09 19:21:05

<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <div class="moz-cite-prefix">Sorry for the delayed take-up on this
      point, but I am now seeing similar symptoms to those reported by
      Yagnesh, running under Wine 1.7, and I came upon this thread. It
      seems the conversion doesn't always fail, but does for some files
      (perhaps depending on size?). To speak to two questions that were
      raised a while back and still appear to be open:<br>
      <ol>
        <li>The conversion of one particular file works fine in an older
          version of PWiz that I had been using, viz. 3.0.5759. It now
          fails as Yagnesh described in a recent version, 3.0.6736. <br>
        </li>
        <li>I'm not a Windows programming expert, but here are a couple
          of posts I found that indicate that the thing for detecting
          Wine is to check for the existence of
          "SOFTWARE\Wine\Wine\Config" in the registry (other methods are
          available, too).</li>
      </ol>
      <blockquote>
        <ul>
          <li><a class="moz-txt-link-freetext" href="http://www.codejuggle.dj/how-to-detect-if-your-windows-application-is-running-under-wine/">http://www.codejuggle.dj/how-to-detect-if-your-windows-application-is-running-under-wine/</a></li>
          <li><a class="moz-txt-link-freetext" href="http://stackoverflow.com/questions/7372388/determine-whether-a-program-is-running-under-wine-at-runtime">http://stackoverflow.com/questions/7372388/determine-whether-a-program-is-running-under-wine-at-runtime</a><br>
          </li>
        </ul>
      </blockquote>
      I'd love to see a solution for Linux, too!<br>
      <br>
      With thanks and best regards,<br>
      <br>
      James Candlin<br>
      <br>
      <br>
      On 07/21/2014 11:03, Chambers, Matthew wrote:<br>
    </div>
    <blockquote cite="mid:%3C5...@gm...%3E" type="cite">
      <meta content="text/html; charset=ISO-8859-1"
        http-equiv="Content-Type">
      I agree. Is there a way to detect that the code is running under
      Wine and I can just branch on that to use the older non-UTF8 code?<br>
      <br>
      -Matt<br>
      <br>
      <br>
      <div class="moz-cite-prefix">On 7/21/2014 12:07 PM, Joseph Slagel
        wrote:<br>
      </div>
      <blockquote
cite="mid:CALAet2Krq=H51==WRs...@ma..."
        type="cite">
        <div dir="ltr">
          <div>That's disappointing to hear as many organizations do
            have significant Linux compute resources.&nbsp; I'm sure I'm not
            alone in wishing the Wine solution would simplify proteomics
            analysis pipelines.<br>
            <br>
          </div>
          -Joe<br>
          <br>
        </div>
        <div class="gmail_extra"><br>
          <br>
          <div class="gmail_quote">On Tue, Jul 15, 2014 at 9:29 AM,
            Chambers, Matthew <span dir="ltr">&lt;<a
                moz-do-not-send="true"
                href="mailto:mat...@gm..." target="_blank">mat...@gm...</a>&gt;</span>
            wrote:<br>
            <blockquote class="gmail_quote" style="margin:0 0 0
              .8ex;border-left:1px #ccc solid;padding-left:1ex">I
              suspect it's the interprocess_exception that's killing it.
              I recently<br>
              changed SHA1 calc to use memory mapped files on Windows to
              support UTF8<br>
              filenames and improve performance. The cross-platform
              implementation is<br>
              provided by boost::interprocess. It's likely that that
              implementation is<br>
              breaking down on Wine, although I don't know.
              Unfortunately, I don't<br>
              really have the bandwidth to support Wine. You can try to
              get an older<br>
              version of pwiz before the SHA1 change and it may work.<br>
              <br>
              Sorry,<br>
              -Matt<br>
              <div class="HOEnZb">
                <div class="h5"><br>
                  <br>
                  On 7/15/2014 10:38 AM, Yagnesh Umrania wrote:<br>
                  &gt; Hello,<br>
                  &gt;<br>
                  &gt; I am trying to run msconvert in linux (ubuntu
                  14.04) with wine 1.7.22.<br>
                  &gt;<br>
                  &gt; However, running msconvert gives a "Error writing
                  run 1" message:<br>
                  &gt;<br>
                  &gt; wine msconvert.exe DR_band1_280514_run1.RAW<br>
                  &gt;<br>
                  &gt; format: mzML<br>
                  &gt; &nbsp; &nbsp; &nbsp; m/z: Compression-None, 64-bit<br>
                  &gt; &nbsp; &nbsp; &nbsp; intensity: Compression-None, 32-bit<br>
                  &gt; &nbsp; &nbsp; &nbsp; rt: Compression-None, 64-bit<br>
                  &gt; ByteOrder_LittleEndian<br>
                  &gt; &nbsp; &nbsp;indexed="true"<br>
                  &gt; outputPath: .<br>
                  &gt; extension: .mzML<br>
                  &gt; contactFilename:<br>
                  &gt;<br>
                  &gt; filters:<br>
                  &gt;<br>
                  &gt; filenames:<br>
                  &gt; &nbsp; &nbsp; DR_band1_280514_run1.RAW<br>
                  &gt;<br>
                  &gt; processing file: DR_band1_280514_run1.RAW<br>
                  &gt; fixme:ntdll:NtLockFile I/O completion on lock not
                  implemented yet<br>
                  &gt; fixme:ntdll:NtQuerySection
                  (0x290,0,0x33eae8,0x00000010,(nil)) stub!<br>
                  &gt; Error writing run 1 in
                  "DR_band1_280514_run1.RAW":<br>
                  &gt; boost::interprocess_exception::library_error<br>
                  &gt;<br>
                  &gt;<br>
                  &gt; Any help would be appreciated!<br>
                  &gt;<br>
                  &gt; Many thanks,<br>
                  &gt; Yagnesh<br>
                  &gt;<br>
                  &gt;<br>
                  &gt;
------------------------------------------------------------------------------<br>
                  &gt; Want fast and easy access to all the code in your
                  enterprise? Index and<br>
                  &gt; search up to 200,000 lines of code with a free
                  copy of Black Duck<br>
                  &gt; Code Sight - the same software that powers the
                  world's largest code<br>
                  &gt; search on Ohloh, the Black Duck Open Hub! Try it
                  now.<br>
                  &gt; <a moz-do-not-send="true"
                    href="http://p.sf.net/sfu/bds" target="_blank">http://p.sf.net/sfu/bds</a><br>
                  &gt; _______________________________________________<br>
                  &gt; proteowizard-support mailing list<br>
                  &gt; <a moz-do-not-send="true"
                    href="mailto:pro...@li...">pro...@li...</a><br>
                  &gt; <a moz-do-not-send="true"
                    href="https://lists.sourceforge.net/lists/listinfo/proteowizard-support"
                    target="_blank">https://lists.sourceforge.net/lists/listinfo/proteowizard-support</a><br>
                  <br>
                  <br>
------------------------------------------------------------------------------<br>
                  Want fast and easy access to all the code in your
                  enterprise? Index and<br>
                  search up to 200,000 lines of code with a free copy of
                  Black Duck<br>
                  Code Sight - the same software that powers the world's
                  largest code<br>
                  search on Ohloh, the Black Duck Open Hub! Try it now.<br>
                  <a moz-do-not-send="true"
                    href="http://p.sf.net/sfu/bds" target="_blank">http://p.sf.net/sfu/bds</a><br>
                  _______________________________________________<br>
                  proteowizard-support mailing list<br>
                  <a moz-do-not-send="true"
                    href="mailto:pro...@li...">pro...@li...</a><br>
                  <a moz-do-not-send="true"
                    href="https://lists.sourceforge.net/lists/listinfo/proteowizard-support"
                    target="_blank">https://lists.sourceforge.net/lists/listinfo/proteowizard-support</a><br>
                </div>
              </div>
            </blockquote>
          </div>
          <br>
          <br clear="all">
          <br>
          -- <br>
          <div dir="ltr">Joe Slagel<br>
            Institute for Systems Biology<br>
            <a moz-do-not-send="true"
              href="mailto:js...@sy..." target="_blank">js...@sy...</a><br>
            (206) 732-1362</div>
        </div>
      </blockquote>
      <br>
    </blockquote>
    <br>
  </body>
</html>

Re: [proteowizard-support] msconvert : unknown exception

From: Yagnesh U. <yu...@ca...> - 2014-07-16 07:58:25

Hello,

Many thanks for your comments Brian. I tried resorting to wine 1.6. This 
time I got:

format: mzML
      m/z: Compression-None, 64-bit
      intensity: Compression-None, 32-bit
      rt: Compression-None, 64-bit
ByteOrder_LittleEndian
   indexed="true"
outputPath: .
extension: .mzML
contactFilename:

filters:

filenames:
    DR_band1_280514_run1.RAW

processing file: DR_band1_280514_run1.RAW
fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
hwnd=(nil), edge=3): stub
fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
hwnd=(nil), edge=1): stub
fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
hwnd=(nil), edge=0): stub
fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
hwnd=(nil), edge=2): stub
[Z:\home\local\LABS\yu206\pwiz\msconvert.exe] Caught unknown exception.
Please report this error to su...@pr....
Attach the command output and this version information in your report:

ProteoWizard release: 3.0.6485 (2014-7-9)
ProteoWizard MSData: 3.0.6485 (2014-7-9)
ProteoWizard Analysis: 3.0.6478 (2014-7-8)
Build date: Jul 11 2014 15:13:19
fixme:process:FlushProcessWriteBuffers : stub


Once again, any help much appreciated.

Many thanks,
Yagnesh.

On 15/07/14 17:01, Brian Pratt wrote:
 > These two lines:
 >
 > fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
 > fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
 >
 > make me think you've hit the limitations of Wine.
 >
 > Perhaps there's a newer version of Wine that implements these windows
 > API points.  Please do report back to the list if you succeed!
 >
 > Brian
 >
 >
 > On Tue, Jul 15, 2014 at 8:38 AM, Yagnesh Umrania <yu...@ca...
 > <mailto:yu...@ca...>> wrote:
 >
 >     Hello,
 >
 >     I am trying to run msconvert in linux (ubuntu 14.04) with wine 
1.7.22.
 >
 >     However, running msconvert gives a "Error writing run 1" message:
 >
 >     wine msconvert.exe DR_band1_280514_run1.RAW
 >
 >     format: mzML
 >          m/z: Compression-None, 64-bit
 >          intensity: Compression-None, 32-bit
 >          rt: Compression-None, 64-bit
 >     ByteOrder_LittleEndian
 >       indexed="true"
 >     outputPath: .
 >     extension: .mzML
 >     contactFilename:
 >
 >     filters:
 >
 >     filenames:
 >        DR_band1_280514_run1.RAW
 >
 >     processing file: DR_band1_280514_run1.RAW
 >     fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
 >     fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
 >     Error writing run 1 in "DR_band1_280514_run1.RAW":
 >     boost::interprocess_exception::library_error
 >
 >
 >     Any help would be appreciated!
 >
 >     Many thanks,
 >     Yagnesh

On 15/07/14 17:01, Brian Pratt wrote:
> These two lines:
>
> fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
>
> make me think you've hit the limitations of Wine.
>
> Perhaps there's a newer version of Wine that implements these windows 
> API points.  Please do report back to the list if you succeed!
>
> Brian
>
>
> On Tue, Jul 15, 2014 at 8:38 AM, Yagnesh Umrania <yu...@ca... 
> <mailto:yu...@ca...>> wrote:
>
>     Hello,
>
>     I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.
>
>     However, running msconvert gives a "Error writing run 1" message:
>
>     wine msconvert.exe DR_band1_280514_run1.RAW
>
>     format: mzML
>          m/z: Compression-None, 64-bit
>          intensity: Compression-None, 32-bit
>          rt: Compression-None, 64-bit
>     ByteOrder_LittleEndian
>       indexed="true"
>     outputPath: .
>     extension: .mzML
>     contactFilename:
>
>     filters:
>
>     filenames:
>        DR_band1_280514_run1.RAW
>
>     processing file: DR_band1_280514_run1.RAW
>     fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
>     fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
>     Error writing run 1 in "DR_band1_280514_run1.RAW":
>     boost::interprocess_exception::library_error
>
>
>     Any help would be appreciated!
>
>     Many thanks,
>     Yagnesh
>
>
>     ------------------------------------------------------------------------------
>     Want fast and easy access to all the code in your enterprise?
>     Index and
>     search up to 200,000 lines of code with a free copy of Black Duck
>     Code Sight - the same software that powers the world's largest code
>     search on Ohloh, the Black Duck Open Hub! Try it now.
>     http://p.sf.net/sfu/bds
>     _______________________________________________
>     proteowizard-support mailing list
>     pro...@li...
>     <mailto:pro...@li...>
>     https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>

Re: [proteowizard-support] msconvert : unknown exception

From: Joseph S. <Jos...@sy...> - 2014-07-16 14:46:44

Yagnesh,

It looks as if you tried a older version of Wine.  You might want to try
the latest version of wine with a older version of Proteowizard.

-Joe


On Wed, Jul 16, 2014 at 12:58 AM, Yagnesh Umrania <yu...@ca...> wrote:

>  Hello,
>
> Many thanks for your comments Brian. I tried resorting to wine 1.6. This
> time I got:
>
> format: mzML
>      m/z: Compression-None, 64-bit
>      intensity: Compression-None, 32-bit
>      rt: Compression-None, 64-bit
> ByteOrder_LittleEndian
>   indexed="true"
> outputPath: .
> extension: .mzML
> contactFilename:
>
> filters:
>
> filenames:
>    DR_band1_280514_run1.RAW
>
> processing file: DR_band1_280514_run1.RAW
> fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
> hwnd=(nil), edge=3): stub
> fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
> hwnd=(nil), edge=1): stub
> fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
> hwnd=(nil), edge=0): stub
> fixme:appbar:handle_appbarmessage SHAppBarMessage(ABM_GETAUTOHIDEBAR,
> hwnd=(nil), edge=2): stub
> [Z:\home\local\LABS\yu206\pwiz\msconvert.exe] Caught unknown exception.
> Please report this error to su...@pr....
> Attach the command output and this version information in your report:
>
> ProteoWizard release: 3.0.6485 (2014-7-9)
> ProteoWizard MSData: 3.0.6485 (2014-7-9)
> ProteoWizard Analysis: 3.0.6478 (2014-7-8)
> Build date: Jul 11 2014 15:13:19
> fixme:process:FlushProcessWriteBuffers : stub
>
>
> Once again, any help much appreciated.
>
> Many thanks,
> Yagnesh.
>
> On 15/07/14 17:01, Brian Pratt wrote:
> > These two lines:
> >
> > fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> > fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
> >
> > make me think you've hit the limitations of Wine.
> >
> > Perhaps there's a newer version of Wine that implements these windows
> > API points.  Please do report back to the list if you succeed!
> >
> > Brian
> >
> >
> > On Tue, Jul 15, 2014 at 8:38 AM, Yagnesh Umrania <yu...@ca...
> > <mailto:yu...@ca...> <yu...@ca...>> wrote:
> >
> >     Hello,
> >
> >     I am trying to run msconvert in linux (ubuntu 14.04) with wine
> 1.7.22.
> >
> >     However, running msconvert gives a "Error writing run 1" message:
> >
> >     wine msconvert.exe DR_band1_280514_run1.RAW
> >
> >     format: mzML
> >          m/z: Compression-None, 64-bit
> >          intensity: Compression-None, 32-bit
> >          rt: Compression-None, 64-bit
> >     ByteOrder_LittleEndian
> >       indexed="true"
> >     outputPath: .
> >     extension: .mzML
> >     contactFilename:
> >
> >     filters:
> >
> >     filenames:
> >        DR_band1_280514_run1.RAW
> >
> >     processing file: DR_band1_280514_run1.RAW
> >     fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> >     fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
> >     Error writing run 1 in "DR_band1_280514_run1.RAW":
> >     boost::interprocess_exception::library_error
> >
> >
> >     Any help would be appreciated!
> >
> >     Many thanks,
> >     Yagnesh
>
> On 15/07/14 17:01, Brian Pratt wrote:
>
> These two lines:
>
> fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
> fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
>
>  make me think you've hit the limitations of Wine.
>
>  Perhaps there's a newer version of Wine that implements these windows
> API points.  Please do report back to the list if you succeed!
>
>  Brian
>
>
> On Tue, Jul 15, 2014 at 8:38 AM, Yagnesh Umrania <yu...@ca...> wrote:
>
>> Hello,
>>
>> I am trying to run msconvert in linux (ubuntu 14.04) with wine 1.7.22.
>>
>> However, running msconvert gives a "Error writing run 1" message:
>>
>> wine msconvert.exe DR_band1_280514_run1.RAW
>>
>> format: mzML
>>      m/z: Compression-None, 64-bit
>>      intensity: Compression-None, 32-bit
>>      rt: Compression-None, 64-bit
>> ByteOrder_LittleEndian
>>   indexed="true"
>> outputPath: .
>> extension: .mzML
>> contactFilename:
>>
>> filters:
>>
>> filenames:
>>    DR_band1_280514_run1.RAW
>>
>> processing file: DR_band1_280514_run1.RAW
>> fixme:ntdll:NtLockFile I/O completion on lock not implemented yet
>> fixme:ntdll:NtQuerySection (0x290,0,0x33eae8,0x00000010,(nil)) stub!
>> Error writing run 1 in "DR_band1_280514_run1.RAW":
>> boost::interprocess_exception::library_error
>>
>>
>> Any help would be appreciated!
>>
>> Many thanks,
>> Yagnesh
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Want fast and easy access to all the code in your enterprise? Index and
>> search up to 200,000 lines of code with a free copy of Black Duck
>> Code Sight - the same software that powers the world's largest code
>> search on Ohloh, the Black Duck Open Hub! Try it now.
>> http://p.sf.net/sfu/bds
>> _______________________________________________
>> proteowizard-support mailing list
>> pro...@li...
>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>>
>
>
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>


-- 
Joe Slagel
Institute for Systems Biology
js...@sy...
(206) 732-1362