<p>Don't use Wine at all! You seem to be running an Ubuntu installation inside a MacOS system using parallels. And then a Windows emulation layer (wine) on top of that. This is a very complex system.</p>

<p>However, the software you are trying to install is written in Java and can run perfectly well on any of the operating systems you have available. So there is absolutely no reason to even try to run it via Wine. Just run it natively on either your MacOS or your Ubuntu. As explained in the page you linked to:</p>

<p>Execute PGDSpider GUI:</p>

<blockquote>
  <ul>
  <li><p>Windows:<br>
  execute the file <code>PGDSpider2.exe</code> to start the program</p></li>
  <li><p>Linux:<br>
  execute the command <code>./PGDSpider2.sh</code> to start the program</p></li>
  <li><p>Mac and others:<br>
  execute the command <code>java -Xmx1024m -Xms512m -jar
  PGDSpider2.jar</code> to start the program</p></li>
  </ul>
</blockquote>

<p>So ignore the Windows instructions and pick either one of the others.</p>

CC BY-SA 3.0
2017-12-30T12:44:23.910Z
2017-12-30T12:44:23.910Z
terdon
<p>I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from <a href="http://www.cmpg.unibe.ch/software/PGDSpider/" rel="nofollow noreferrer">here</a>. Essentially the program is supposed to convert different file formats used for bioinformatics.</p>

<p>I'm running it in a 32-bit wine server and I have the Java V.9 and the Microsoft.net packages downloaded on that same server. I've been getting this error.</p>

<p>I have tried the installation on a clean bottle but get the same following error, any thoughts?</p>

<pre><code>parallels@ubuntu:~/.wine32/drive_c/Program Files/PGDSpider_2.1.1.3$ WINEPREFIX=~/.wine32 wine PGDSpider2.exe
fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
fixme:process:SetProcessDEPPolicy (1): stub
fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
fixme:process:SetProcessShutdownParameters (00000380, 00000000): partial stub.
fixme:process:GetProcessWorkingSetSize (0xffffffff,0x73e94c,0x73e950): stub
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e6fc,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
parallels@ubuntu:~/.wine32/drive_c/Program Files/PGDSpider_2.1.1.3$ fixme:win:EnumDisplayDevicesW ((null),0,0x39edcf0,0x00000000), stub!
fixme:win:EnumDisplayDevicesW ((null),1,0x39edcf0,0x00000000), stub!
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  156 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  241
  Current serial number in output stream:  241
k
fixme:advapi:RegisterEventSourceW ((null),L".NET Runtime Optimization Service"): stub
fixme:advapi:DeregisterEventSource (0xcafe4242) stub
</code></pre>

CC BY-SA 3.0
2017-12-02T15:47:25.980Z
According to this [forum](https://forum.winehq.org/viewtopic.php?t=7048) it is likely a problem with the wine configuration of the video card drivers or opengl. I would suggest posting on a forum for wine as I don't think this is an issue with PGDSpider.
Bioathlete
CC BY-SA 3.0
2017-12-30T12:35:45.670Z
@gringer the [community consensus](https://bioinformatics.meta.stackexchange.com/q/132/298) is that questions asking for help installing bioinformatics software are on topic since they're often non-trivial to install. I agree that this is a complex case, and it might be easier to find an answer on sites like [apple.se], [ubuntu.se] or [su], but that does not make it off topic here.
terdon
CC BY-SA 3.0
2017-12-30T12:37:09.140Z
Mollie, while this is on topic here as I explain above, you might want to consider deleting it and asking instead on either [apple.se] or [ubuntu.se]. In either case, please [edit] to explain whether your Ubuntu is actually running on your mac hardware or if it is running using the parallels virtualization tool. It looks like the latter and that is relevant.
terdon
CC BY-SA 3.0
2017-12-30T12:38:58.063Z
Also, why in the world are you trying to run the Windows version of this? The website you linked to provides both a MacOS and a Linux version. Either of those would be simpler to use than trying to run it through Wine. Don't make your life harder than it needs to be!
terdon
<format-conversion><linux><phylogenetics><molecular-genetics><mtdna>
Unable to Install PGDSpider using Ubuntu and wine
# Unable to Install PGDSpider using Ubuntu and wine

(Asked by: username_0 on 2017-12-01)

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for bioinformatics.
I'm running it in a 32-bit wine server and I have the Java V.9 and the Microsoft.net packages downloaded on that same server. I've been getting this error.
I have tried the installation on a clean bottle but get the same following error, any thoughts?
parallels@ubuntu:~/.wine32/drive_c/Program Files/PGDSpider_2.1.1.3$ WINEPREFIX=~/.wine32 wine PGDSpider2.exe
fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
fixme:process:SetProcessDEPPolicy (1): stub
fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
fixme:process:SetProcessShutdownParameters (00000380, 00000000): partial stub.
fixme:process:GetProcessWorkingSetSize (0xffffffff,0x73e94c,0x73e950): stub
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e6fc,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
fixme:win:RegisterDeviceNotificationA (hwnd=0x12dd30, filter=0x93e698,flags=0x00000001) returns a fake device notification handle!
fixme:win:UnregisterDeviceNotification (handle=0xcafecafe), STUB!
parallels@ubuntu:~/.wine32/drive_c/Program Files/PGDSpider_2.1.1.3$ fixme:win:EnumDisplayDevicesW ((null),0,0x39edcf0,0x00000000), stub!
fixme:win:EnumDisplayDevicesW ((null),1,0x39edcf0,0x00000000), stub!
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  156 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  241
  Current serial number in output stream:  241
k
fixme:advapi:RegisterEventSourceW ((null),L".NET Runtime Optimization Service"): stub
fixme:advapi:DeregisterEventSource (0xcafe4242) stub

**Tags:** format-conversion, linux, phylogenetics, molecular-genetics, mtdna
> **Comments:**
> **username_1**: According to this [forum](https://forum.winehq.org/viewtopic.php?t=7048) it is likely a problem with the wine configuration of the video card drivers or opengl. I would suggest posting on a forum for wine as I don't think this is an issue with PGDSpider.  
> **username_2**: @gringer the [community consensus](https://bioinformatics.meta.stackexchange.com/q/132/298) is that questions asking for help installing bioinformatics software are on topic since they're often non-trivial to install. I agree that this is a complex case, and it might be easier to find an answer on sites like [apple.se], [ubuntu.se] or [su], but that does not make it off topic here.  
> **username_2**: Mollie, while this is on topic here as I explain above, you might want to consider deleting it and asking instead on either [apple.se] or [ubuntu.se]. In either case, please [edit] to explain whether your Ubuntu is actually running on your mac hardware or if it is running using the parallels virtualization tool. It looks like the latter and that is relevant.  
> **username_2**: Also, why in the world are you trying to run the Windows version of this? The website you linked to provides both a MacOS and a Linux version. Either of those would be simpler to use than trying to run it through Wine. Don't make your life harder than it needs to be!  

---

## 1 answers

### Answer by username_2 on 2017-12-30. Score: 1

Don't use Wine at all! You seem to be running an Ubuntu installation inside a MacOS system using parallels. And then a Windows emulation layer (wine) on top of that. This is a very complex system.

However, the software you are trying to install is written in Java and can run perfectly well on any of the operating systems you have available. So there is absolutely no reason to even try to run it via Wine. Just run it natively on either your MacOS or your Ubuntu. As explained in the page you linked to:

Execute PGDSpider GUI:

> * Windows:  
>   execute the file `PGDSpider2.exe` to start the program
> * Linux:  
>   execute the command `./PGDSpider2.sh` to start the program
> * Mac and others:  
>   execute the command `java -Xmx1024m -Xms512m -jar
>   PGDSpider2.jar` to start the program

So ignore the Windows instructions and pick either one of the others.


---

