[Bug 41124] New: Proteowizard/msconvert command line tool hangs

https://bugs.winehq.org/show_bug.cgi?id=41124

            Bug ID: 41124
           Summary: Proteowizard/msconvert command line tool hangs
           Product: Wine
           Version: 1.9.16
          Hardware: x86-64
                OS: Linux
            Status: UNCONFIRMED
          Severity: normal
          Priority: P2
         Component: -unknown
          Assignee: wine-bugs(a)winehq.org
          Reporter: sneumann(a)ipb-halle.de
      Distribution: ---

Created attachment 55331
  --> https://bugs.winehq.org/attachment.cgi?id=55331
Logfile with wine output

I am trying to get a command line tool to run under wine, and have varied
success. The command msconvert.exe is part 
of the mixed open/closed source Proteowizard project [1], which provides a
unified access to the mass spectrometry data 
from any instrument vendor through their closed source data access DLLs. In
particular, msconvert converts into 
vendor-neutral open XML formats. Download available from [2].

So success or failure running msconvert depends on which and how these DLLs are
written and called, which I have no direct control of.

* I can run msconvert just fine when converting from one open format to
another, which does not require any closed DLLs. 
  So msconvert itself is fine. 

* I have one instrument that has a mix of *.dll that are identified as "PE32
executable (DLL)" for console and GUI,
  and also include Mono/.Net assemblies. Runs fine.

* I have data and DLLs for a different instrument, where at runtime a few
err:ole messages are suspicious 
  to my (wine-untrained) eye, see also full trace below:

        err:ole:marshal_object Failed to create an IRpcStubBuffer from
IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
        err:ole:ClientIdentity_QueryMultipleInterfaces
IRemUnknown_RemQueryInterface failed with error 0x80004002

  A few output lines later the process just hangs, it can be terminated with
^C.

I am running Ubuntu 16.04, and previously 14.04, and I have tried Wine Staging
1.9.16~ubuntu16.04.1 and 1:1.8.0-0ubuntu1~ubuntu15.10.1~ppa1
(and wine-1.6.2 earlier). Needless to say, works under Windows.
The msconvert sources are living under [3]. Im using an WINEARCH=win32
wineprefix. Dependencies I know of/guess are installed via a recent winetricks
(20160724).

  rm -rf .wine
  export WINEARCH=win32

  winetricks --unattended msxml3 mfc42 corefonts
  winetricks --unattended vcrun2005
  winetricks --unattended vcrun2008
  winetricks --unattended vcrun2010
  winetricks --unattended dotnet35sp1
  winetricks --unattended dotnet40

  # http://proteowizard.sourceforge.net/downloads.shtml
  msiexec /i  pwiz-setup.msi

and then running on a small file [4] hangs:

  wine ./msconvert.exe small.RAW
  [logs attached separately]

Andrew Udvare gave an excellent assessment [5] of my debugging output
on the mailling list, copied in here:

On Mo, 2016-08-01 at 03:32 -0700, Andrew Udvare wrote:
> > On 2016-08-01, at 02:51, Steffen Neumann <sneumann(a)ipb-halle.de>
> > wrote:
> >
> > err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
> > err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
>
> Definitely file a bug. There is sort of this related one, but it has
> to do with InstallShield: https://bugs.winehq.org/show_bug.cgi?id=24611
>
> Maybe some useful information:
>
> https://msdn.microsoft.com/en-us/library/windows/desktop/ms678504(v=vs.85).a...
>
> E_NOINTERFACE	0x80004002	Interface not supported.
>
> Your OLE32 errors:
>
> https://source.winehq.org/git/wine.git/blob/HEAD:/dlls/ole32/marshal.c#l168
> https://source.winehq.org/git/wine.git/blob/HEAD:/dlls/ole32/marshal.c#l305
>
> Something is wrong with Wine and IRunnableObject for this use case.
> And it seems your app does not check the return when it queries
> interfaces? I presume that is why more errors just come later about
> not correctly running within an apartment.
>
> IRunnableObject = {00000126-0000-0000-c000-000000000046} -> https://msdn.microsoft.com/en-
> us/library/windows/desktop/ms692783%28v=vs.85%29.aspx?f=255&MSPPError=-2147217396
>
> DCOM as done in Wine is described a bit here: https://www.winehq.org/docs/winedev-guide/dcom-1
> --
> Andrew Udvare

Running msconvert under wine has long been a challenge, with Wine reports in
#24761 [6] and #29900 [7] that have been
fixed/markeddupes/closed by now, but it doesn't work for me. An old wiki
entry[8] with earlier 
versions of both wine and msconvert reports success by someone for files such
as mine.

Happy to help with debugging,
yours,
Steffen

[1] http://proteowizard.sourceforge.net/
[2] http://proteowizard.sourceforge.net/downloads.shtml
[3] https://sourceforge.net/p/proteowizard/code/HEAD/tree/trunk/pwiz/
[4] http://proteowizard.sourceforge.net/example_data/small.RAW
[5] https://www.winehq.org/pipermail/wine-users/2016-August/107380.html
[6] https://bugs.winehq.org/show_bug.cgi?id=24761
[7] https://bugs.winehq.org/show_bug.cgi?id=29900
[8] http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine

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[Bug 41124] Proteowizard/msconvert command line tool hangs

https://bugs.winehq.org/show_bug.cgi?id=41124

sneumann(a)ipb-halle.de changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |audvare(a)gmail.com
       Distribution|---                         |Ubuntu

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