Building micro-manager on ubuntu 18.04

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Building micro-manager on ubuntu 18.04

Aurélien Courtois
Dear all,
I am sorry if my question is trivial, I have not much experience with building manager in Unix system, but I am trying to install micromanager on Ubuntu 18.04 following all steps on "https://protect2.fireeye.com/url?k=bc76ace2-e03699dc-bc768bff-0cc47ad9c120-aec5d09e9fba3b48&u=https://micro-manager.org/wiki/Linux_installation_from_source_(Ubuntu)" and i get this error message after "make":

> mmstudio.compile:
>   [mm-javac] Compiling 272 source files to /home/aure/mm/micro-manager1.4/mmstudio/build
>   [mm-javac] warning: [options] bootstrap class path not set in conjunction with -source 6
>   [mm-javac] warning: [options] source value 6 is obsolete and will be removed in a future release
>   [mm-javac] warning: [options] target value 1.6 is obsolete and will be removed in a future release
>   [mm-javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/navigation/CenterAndDragListener.java:11: warning: [deprecation] Event in java.awt has been deprecated
>   [mm-javac] import java.awt.Event;
>   [mm-javac]                ^
>   [mm-javac] warning: No processor claimed any of these annotations: com.google.common.eventbus.Subscribe
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/navigation/CenterAndDragListener.java:11: warning: [deprecation] Event in java.awt has been deprecated
>   [mm-javac] import java.awt.Event;
>   [mm-javac]                ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:26: error: package loci.common does not exist
>   [mm-javac] import loci.common.DateTools;
>   [mm-javac]                   ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:27: error: package loci.common.services does not exist
>   [mm-javac] import loci.common.services.ServiceFactory;
>   [mm-javac]                            ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:28: error: package loci.formats does not exist
>   [mm-javac] import loci.formats.MetadataTools;
>   [mm-javac]                    ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:29: error: package loci.formats.meta does not exist
>   [mm-javac] import loci.formats.meta.IMetadata;
>   [mm-javac]                         ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:30: error: package loci.formats.services does not exist
>   [mm-javac] import loci.formats.services.OMEXMLService;
>   [mm-javac]                             ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error: package ome.units does not exist
>   [mm-javac] import ome.units.UNITS;
>   [mm-javac]                 ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:32: error: package ome.units.quantity does not exist
>   [mm-javac] import ome.units.quantity.Length;
>   [mm-javac]                          ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:33: error: package ome.units.quantity does not exist
>   [mm-javac] import ome.units.quantity.Time;
>   [mm-javac]                          ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:47: error: cannot find symbol
>   [mm-javac]    private IMetadata metadata_;
>   [mm-javac]            ^
>   [mm-javac]   symbol:   class IMetadata
>   [mm-javac]   location: class OMEMetadata
>   [mm-javac] 9 errors
>   [mm-javac] 7 warnings
>
> BUILD FAILED
> /home/aure/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.
>
> Total time: 2 seconds
> Makefile:888: recipe for target 'MMJ_.jar' failed
> make[1]: *** [MMJ_.jar] Error 1
> make[1]: Leaving directory '/home/aure/mm/micro-manager1.4/mmstudio'
> Makefile:521: recipe for target 'all-recursive' failed
> make: *** [all-recursive] Error 1


(ps; i am using openjdk-11-jdk, except this everything is done exactly the same way as in the instruction, i tried also with openjdk-8-jdk instead of 11.)

And i am quite lost, i have no idea what causes this and what i can do to manage to build micromanager. I would be very thankful if you could help me or orient me to other posts about similar problems, that i unfortunately couldn't find.
Best,
 Aurelien


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Re: Building micro-manager on ubuntu 18.04

T1000

Hi Aurélien,

 

I am using same Jave version on Ubuntu 18 without any problem.  But I am facing same issue on Mac.

 

javabuild.xml:110:

 

I have alrady posted this yesterday. I hope will get futher hint to fix this issue today.

 

 

BR

Ravi

 

-----Ursprüngliche Nachricht-----
Von: "Aurélien Courtois" [[hidden email]]
Gesendet: Mi. 08.05.2019 09:38
An: [hidden email]
Betreff: [micro-manager-general] Building micro-manager on ubuntu 18.04

Dear all,
I am sorry if my question is trivial, I have not much experience with building manager in Unix system, but I am trying to install micromanager on Ubuntu 18.04 following all steps on "https://protect2.fireeye.com/url?k=bc76ace2-e03699dc-bc768bff-0cc47ad9c120-aec5d09e9fba3b48&u=https://micro-manager.org/wiki/Linux_installation_from_source_(Ubuntu)" and i get this error message after "make":

> mmstudio.compile:
>   [mm-javac] Compiling 272 source files to /home/aure/mm/micro-manager1.4/mmstudio/build
>   [mm-javac] warning: [options] bootstrap class path not set in conjunction with -source 6
>   [mm-javac] warning: [options] source value 6 is obsolete and will be removed in a future release
>   [mm-javac] warning: [options] target value 1.6 is obsolete and will be removed in a future release
>   [mm-javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/navigation/CenterAndDragListener.java:11: warning: [deprecation] Event in java.awt has been deprecated
>   [mm-javac] import java.awt.Event;
>   [mm-javac]                ^
>   [mm-javac] warning: No processor claimed any of these annotations: com.google.common.eventbus.Subscribe
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/navigation/CenterAndDragListener.java:11: warning: [deprecation] Event in java.awt has been deprecated
>   [mm-javac] import java.awt.Event;
>   [mm-javac]                ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:26: error: package loci.common does not exist
>   [mm-javac] import loci.common.DateTools;
>   [mm-javac]                   ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:27: error: package loci.common.services does not exist
>   [mm-javac] import loci.common.services.ServiceFactory;
>   [mm-javac]                            ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:28: error: package loci.formats does not exist
>   [mm-javac] import loci.formats.MetadataTools;
>   [mm-javac]                    ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:29: error: package loci.formats.meta does not exist
>   [mm-javac] import loci.formats.meta.IMetadata;
>   [mm-javac]                         ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:30: error: package loci.formats.services does not exist
>   [mm-javac] import loci.formats.services.OMEXMLService;
>   [mm-javac]                             ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error: package ome.units does not exist
>   [mm-javac] import ome.units.UNITS;
>   [mm-javac]                 ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:32: error: package ome.units.quantity does not exist
>   [mm-javac] import ome.units.quantity.Length;
>   [mm-javac]                          ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:33: error: package ome.units.quantity does not exist
>   [mm-javac] import ome.units.quantity.Time;
>   [mm-javac]                          ^
>   [mm-javac] /home/aure/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:47: error: cannot find symbol
>   [mm-javac]    private IMetadata metadata_;
>   [mm-javac]            ^
>   [mm-javac]   symbol:   class IMetadata
>   [mm-javac]   location: class OMEMetadata
>   [mm-javac] 9 errors
>   [mm-javac] 7 warnings
>
> BUILD FAILED
> /home/aure/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.
>
> Total time: 2 seconds
> Makefile:888: recipe for target 'MMJ_.jar' failed
> make[1]: *** [MMJ_.jar] Error 1
> make[1]: Leaving directory '/home/aure/mm/micro-manager1.4/mmstudio'
> Makefile:521: recipe for target 'all-recursive' failed
> make: *** [all-recursive] Error 1
(ps; i am using openjdk-11-jdk, except this everything is done exactly the same way as in the instruction, i tried also with openjdk-8-jdk instead of 11.)

And i am quite lost, i have no idea what causes this and what i can do to manage to build micromanager. I would be very thankful if you could help me or orient me to other posts about similar problems, that i unfortunately couldn't find.
Best,
 Aurelien

-----Ursprüngliche Nachricht Ende-----




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