compiling MM2

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compiling MM2

julou
Hello,

Until last week, I used to be able to compile MM2 from source on a centos server (and as far as I remember, mm2 was the default branch on github).
Now, I have to checkout to the mm2 branch and the build doesn't work anymore: I get no error message but running mmimagej only starts imagej, then manually clicking on MM studio in the plugin menu doesn't open the MM GUI either… I get the  error below in the shell…

Was there any change on the github repo? any breaking change on the mm2 branch?
Thanks a lot for you help. Best,

Thomas


2016-07-13T14:22:17.609403 tid139931869079296 [IFO,LogManager] Enabled logging to stderr
2016-07-13T14:22:17.619593 tid139931869079296 [IFO,App] EDTHangLogger: Stopping monitoring of EDT hangs
2016-07-13T14:22:17.619571 tid139931869079296 [IFO,LogManager] Enabled primary log file /tmp/CoreLog20160713T142217_pid31876.txt
2016-07-13T14:22:17.620024 tid139931869079296 [IFO,App] EDTHangLogger: Started monitoring of EDT hangs
                                              [       ] [heartbeat timeout = 4500 ms, hang check interval = 1000 ms]
2016-07-13T14:22:17.620033 tid139931869079296 [IFO,App] User: julou
2016-07-13T14:22:17.620040 tid139931869079296 [IFO,App] Host: login13.cluster.bc2.ch
2016-07-13T14:22:17.620045 tid139931869079296 [IFO,App] MM Studio version: 2.0.x dev
2016-07-13T14:22:17.620053 tid139931869079296 [IFO,App] MMCore version 8.3.0
2016-07-13T14:22:17.620058 tid139931869079296 [IFO,App] Device API version 67, Module API version 10
2016-07-13T14:22:17.620063 tid139931869079296 [IFO,App] Operating System: Linux (amd64) 2.6.32-431.29.2.el6.x86_64
2016-07-13T14:22:17.620066 tid139931869079296 [IFO,App] JVM: Java HotSpot(TM) 64-Bit Server VM, version 1.7.0_80, 64-bit
2016-07-13T14:22:17.646824 tid139931869079296 [IFO,App] 
                                              [       ] bsh.InterpreterError: set: Field access: bsh.ReflectError: No such field: console : at Line: -1 : in file: <Called from Java Code> : <Compiled Java Code>
                                              [       ]  in Thread[AWT-EventQueue-0,6,main]
                                              [       ]   at bsh.Interpreter.setu(Unknown Source)
                                              [       ]   at bsh.Interpreter.setConsole(Unknown Source)
                                              [       ]   at org.micromanager.internal.script.ScriptPanel.resetInterpreter(ScriptPanel.java:1488)
                                              [       ]   at org.micromanager.internal.script.ScriptPanel.<init>(ScriptPanel.java:752)
                                              [       ]   at org.micromanager.internal.MMStudio.createScriptPanel(MMStudio.java:818)
                                              [       ]   at org.micromanager.internal.MMStudio.initializationSequence(MMStudio.java:375)
                                              [       ]   at org.micromanager.internal.MMStudio.<init>(MMStudio.java:317)
                                              [       ]   at MMStudioPlugin$1.run(MMStudioPlugin.java:82)
                                              [       ]   at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
                                              [       ]   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
                                              [       ]   at java.awt.EventQueue.access$300(EventQueue.java:103)
                                              [       ]   at java.awt.EventQueue$3.run(EventQueue.java:706)
                                              [       ]   at java.awt.EventQueue$3.run(EventQueue.java:704)
                                              [       ]   at java.security.AccessController.doPrivileged(Native Method)
                                              [       ]   at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
                                              [       ]   at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
                                              [       ]   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
                                              [       ]   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
                                              [       ]   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
                                              [       ]   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)                                              [       
                                              [       ]   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
                                              [       ]   at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: compiling MM2

Mark Tsuchida-2
Hi Thomas,

On Wed, Jul 13, 2016 at 5:28 AM, julou <[hidden email]> wrote:
Until last week, I used to be able to compile MM2 from source on a centos
server (and as far as I remember, mm2 was the default branch on github).
Now, I have to checkout to the mm2 branch and the build doesn't work
anymore: I get no error message but running mmimagej only starts imagej,
then manually clicking on MM studio in the plugin menu doesn't open the MM
GUI either… I get the  error below in the shell…


It's hard to say without seeing your ./configure flags (see config.log), but make sure there is no bsh-*.jar or BeanShell.jar in your install destination before you run 'make install'.

mm2 has never been the default branch on GitHub (it probably will be in the future). 'master', the default, will give you Micro-Manager 1.4.

It is always possible for the build to end up in a bad state when continually updating the source. Starting over with a fresh source tree might help.
First try 'make clean' and 'autoreconf'.
If that doesn't fix it, you can do 'git clean -dxf' and start over from ./autogen.sh.

Best,
Mark

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Re: compiling MM2

julou
Hi Mark,

Sorry for the very delayed answer… I guess I hoped the problem would go with a few more commits, or with some other magic. But it didn't :(

I followed  your instructions:
'git clean -dxf'
'make clean'  'autoreconf'
then redoing all steps…

I also tried to clone the repo form scratch. Nothing helps always the same error related to beanshell (and no: there's no other jar than ij.jar when I start the 'make install' step)…
I attach the config.log file, with some hope it will help you figure out what we do wrong.

Thanks for your help. Best,
Thomas
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: compiling MM2

Egor Zindy
In reply to this post by Mark Tsuchida-2
Hi everyone,

On 20 September 2016 at 15:19, julou <[hidden email]> wrote:

> Hi Mark,
>
> Sorry for the very delayed answer… I guess I hoped the problem would go with
> a few more commits, or with some other magic. But it didn't :(
>
> I followed  your instructions:
> 'git clean -dxf'
> 'make clean'  'autoreconf'
> then redoing all steps…
>
> I also tried to clone the repo form scratch. Nothing helps always the same
> error related to beanshell (and no: there's no other jar than ij.jar when I
> start the 'make install' step)…
> I attach the  config.log
> <http://micro-manager.3463995.n2.nabble.com/file/n7587609/config.log>
> file, with some hope it will help you figure out what we do wrong.
>
> Thanks for your help. Best,
> Thomas
>
Same situation here. I am trying to compile mm2 on mint-18 (config.log
attached).

As per thread, I unzipped a clean ij149v just before make fetchdeps /
make / make install.

The micro-manager startup configuration dialog does come up, then if I
press OK, it disappears but the mmstudio frame doesn't appear. I can
close ImageJ using the File->Quit menu though.

mm14 compiles and runs fine by the way.

Kind regards,
Egor

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CoreLog20161009T131554_pid2114.txt (13K) Download Attachment
config.log.gz (13K) Download Attachment
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Re: compiling MM2

Egor Zindy
Just a quick follow-up...

On 9 October 2016 at 14:24, Egor Zindy <[hidden email]> wrote:

> Hi everyone,
>
> On 20 September 2016 at 15:19, julou <[hidden email]> wrote:
>> Hi Mark,
>>
>> Sorry for the very delayed answer… I guess I hoped the problem would go with
>> a few more commits, or with some other magic. But it didn't :(
>>
>> I followed  your instructions:
>> 'git clean -dxf'
>> 'make clean'  'autoreconf'
>> then redoing all steps…
>>
>> I also tried to clone the repo form scratch. Nothing helps always the same
>> error related to beanshell (and no: there's no other jar than ij.jar when I
>> start the 'make install' step)…
>> I attach the  config.log
>> <http://micro-manager.3463995.n2.nabble.com/file/n7587609/config.log>
>> file, with some hope it will help you figure out what we do wrong.
>>
>> Thanks for your help. Best,
>> Thomas
>>
>
> Same situation here. I am trying to compile mm2 on mint-18 (config.log
> attached).
>
> As per thread, I unzipped a clean ij149v just before make fetchdeps /
> make / make install.
>
> The micro-manager startup configuration dialog does come up, then if I
> press OK, it disappears but the mmstudio frame doesn't appear. I can
> close ImageJ using the File->Quit menu though.
>
> mm14 compiles and runs fine by the way.
>
Commenting out line 1489 of
mmstudio/src/main/java/org/micromanager/internal/script/ScriptPanel.java

     // Apparently clear() also erases bsh.console, which we need
      //beanshellREPLint_.setConsole(cons_);

... seems to fix the problem. Or at least, the MM window shows-up.
I've attached the new CoreLog.

Kind regards,
Egor

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Re: compiling MM2

julou
Egor Zindy wrote
Commenting out line 1489 of mmstudio/src/main/java/org/micromanager/internal/script/ScriptPanel.java seems to fix the problem.
I can (finally) confirm that this also fixes the issue here (using centos 6). Thanks a lot, Egor!
As far as I can say, the compiled version of MM is fully functional, I can also open the script panel, load scripts, etc.

Would it be possible that this issue is addressed by the dev team so that the change can be committed? (I suspect that there might be slightly more required than just commenting a line, unless we're lucky and it's only a left over…) It would be nice to be able to compile the last version without fixing this file every time…

Thank you in advance fro your support. Best,
Thomas

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Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 207 16 21
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: compiling MM2

Hadrien Mary
I am facing the same issue here. Is it going to be fixed ? (I can make a PR if needed) 


--
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Postdoc

Brouhard's lab
University of McGill
Montreal, Canada

On 18 October 2016 at 03:36, julou <[hidden email]> wrote:
Egor Zindy wrote
> Commenting out line 1489 of
> mmstudio/src/main/java/org/micromanager/internal/script/ScriptPanel.java
> seems to fix the problem.

I can (finally) confirm that this also fixes the issue here (using centos
6). Thanks a lot, Egor!
As far as I can say, the compiled version of MM is fully functional, I can
also open the script panel, load scripts, etc.

Would it be possible that this issue is addressed by the dev team so that
the change can be committed? (I suspect that there might be slightly more
required than just commenting a line, unless we're lucky and it's only a
left over…) It would be nice to be able to compile the last version without
fixing this file every time…

Thank you in advance fro your support. Best,
Thomas

--
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University
of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  <a href="tel:%2B41%20%280%2961%20207%2016%2021" value="+41612071621">+41 (0)61 207 16 21




-----
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Re: compiling MM2

julou
Good to see I'm not the only one…
Did you manage to understand the implication of commenting this line out?
Because making a PR for the comment, I could also do but I feared that it would break some script editor features…

Best, Thomas
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: compiling MM2

Hadrien Mary
I don't understand what is causing the error.

However I don't have the error when launching MM from Netbeans...


--
Hadrien Mary
Postdoc

Brouhard's lab
University of McGill
Montreal, Canada

On 4 December 2016 at 15:35, julou <[hidden email]> wrote:
Good to see I'm not the only one…
Did you manage to understand the implication of commenting this line out?
Because making a PR for the comment, I could also do but I feared that it
would break some script editor features…

Best, Thomas



-----
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  <a href="tel:%2B41%20%280%2961%20267%2016%2021" value="+41612671621">+41 (0)61 267 16 21

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Re: compiling MM2

Nico Stuurman-2
In reply to this post by julou

Hi linux users,


On 10/18/16 12:36 AM, julou wrote:
Egor Zindy wrote
Commenting out line 1489 of
mmstudio/src/main/java/org/micromanager/internal/script/ScriptPanel.java
seems to fix the problem. 
I can (finally) confirm that this also fixes the issue here (using centos
6). Thanks a lot, Egor!
As far as I can say, the compiled version of MM is fully functional, I can
also open the script panel, load scripts, etc.

I opened a branch on github that attempts to fix this issue, not by deleting the line but by catching the error that was reported.  Could any of you linux users out there (sorry, I do not have a box ready to test this) try to build the code from:

https://github.com/nicost/micro-manager.git

and let me know if that fixes the issue for you?  I so, I'll create a pull request for the mm2 branch on github.

Best,

Nico


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Re: compiling MM2

Hadrien Mary
Thank you nico.

I confirm the fix on my system. See the log : 

2016-12-13T17:50:13.131053 tid140028895934208 [IFO,Core] Default stage set to Z
2016-12-13T17:50:13.134022 tid140028895934208 [IFO,Core] Did update system state cache
2016-12-13T17:50:13.141715 tid140028895934208 [IFO,Core] Did update system state cache
2016-12-13T17:50:13.305318 tid140028895934208 [IFO,Core] Default autofocus set to Autofocus
2016-12-13T17:50:13.781814 tid140028895934208 [IFO,App] Error: Called to Beanshell setConsole failed. Probably inocuous.set: Field access: bsh.ReflectError: No such field: console : at Line: -1 : in file: <Called from Java Code> : <Compiled Java Code>
2016-12-13T17:50:14.371514 tid140028895934208 [IFO,App] Error: Unrecognized save mode Image Stack File per XY Positions
2016-12-13T17:50:14.371783 tid140028895934208 [IFO,App] Error: Unrecognized save mode null



--
Hadrien Mary
Postdoc

Brouhard's lab
University of McGill
Montreal, Canada

On 13 December 2016 at 17:02, Nico Stuurman <[hidden email]> wrote:

Hi linux users,


On 10/18/16 12:36 AM, julou wrote:
Egor Zindy wrote
Commenting out line 1489 of
mmstudio/src/main/java/org/micromanager/internal/script/ScriptPanel.java
seems to fix the problem. 
I can (finally) confirm that this also fixes the issue here (using centos
6). Thanks a lot, Egor!
As far as I can say, the compiled version of MM is fully functional, I can
also open the script panel, load scripts, etc.

I opened a branch on github that attempts to fix this issue, not by deleting the line but by catching the error that was reported.  Could any of you linux users out there (sorry, I do not have a box ready to test this) try to build the code from:

https://github.com/nicost/micro-manager.git

and let me know if that fixes the issue for you?  I so, I'll create a pull request for the mm2 branch on github.

Best,

Nico


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Re: compiling MM2

Nico Stuurman-2

On 12/13/16 2:50 PM, Hadrien Mary wrote:
> Thank you nico.
>
> I confirm the fix on my system. See the log :

Great!  I submitted a Pull request obn github.

Best,

Nico


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Re: compiling MM2

julou
great news!
thanks a lot :)

Thomas

On 14 Dec 2016, at 01:03, Nico Stuurman-2 [via Micro-Manager] <[hidden email]> wrote:


On 12/13/16 2:50 PM, Hadrien Mary wrote:
> Thank you nico.
>
> I confirm the fix on my system. See the log :

Great!  I submitted a Pull request obn github.

Best,

Nico


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