Re: MM build on Mac

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Re: MM build on Mac

T1000

Hallo Nico,

 

if I try to build aginst Java jdk-12.0.1.jdk I get following error:

 

Making all in mmstudio
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home/ /usr/local/bin/ant -Dmm.javacflags="-Xlint:all,-path,-serial" -logger org.apache.tools.ant.listener.SimpleBigProjectLogger jar
Buildfile: /Users/support/mm/micro-manager1.4/mmstudio/build.xml

mmstudio.compile:
 [mm-javac] Compiling 272 source files to /Users/support/mm/micro-manager1.4/mmstudio/build
 [mm-javac] warning: [options] bootstrap class path not set in conjunction with -source 6
 [mm-javac] error: Source option 6 is no longer supported. Use 7 or later.
 [mm-javac] error: Target option 6 is no longer supported. Use 7 or later.

BUILD FAILED
/Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.

Total time: 0 seconds
make[1]: *** [MMJ_.jar] Error 1
make: *** [all-recursive] Error 1

 

 

 

I changed the Java version:

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/


/Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.

Total time: 3 seconds
make[1]: *** [MMJ_.jar] Error 1
make: *** [all-recursive] Error 1
sh-3.2# make | grep error
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error: package ome.units does not exist
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:32: error: package ome.units.quantity does not exist
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:33: error: package ome.units.quantity does not exist
 [mm-javac] 3 errors

BUILD FAILED
/Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.

Total time: 2 seconds
make[1]: *** [MMJ_.jar] Error 1
make: *** [all-recursive] Error 1

 

so my question, what  do you use on mac?

 

 

Best regards,

Ravi

 

 

 

 

-----Ursprüngliche Nachricht-----
Von: "Stephen J. Arpie via micro-manager-general" [[hidden email]]
Gesendet: Di. 07.05.2019 20:46
An: "Micro-Manager General" [[hidden email]]
Kopie: "Stephen J. Arpie" [[hidden email]]
Betreff: Re: [micro-manager-general] MM build on Mac

I would like on a Mac too.  Let me know how you make out..

Stephen Arpie
203-675-9010
PO Box 230
Guilford, CT 06437




On May 7, 2019, at 2:37 PM, [hidden email] wrote:

 



Dear all,

 

I am try to build Micro Manager on Mac os.  I am getting following error while ruinng make. do you know what I need to do to fix the issue?

 

mm/_micromanager/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:27: error: package loci.common.services does not exist

 

Thanks in advance.

 


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




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Re: MM build on Mac

Stuurman, Nico
On 5/16/19 11:31 AM, [hidden email] wrote:

>
> if I try to build aginst Java jdk-12.0.1.jdk I get following error:
>
> Making all in mmstudio
> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home/
> /usr/local/bin/ant -Dmm.javacflags="-Xlint:all,-path,-serial" -logger
> org.apache.tools.ant.listener.SimpleBigProjectLogger jar
> Buildfile: /Users/support/mm/micro-manager1.4/mmstudio/build.xml
>
> mmstudio.compile:
>  [mm-javac] Compiling 272 source files to
> /Users/support/mm/micro-manager1.4/mmstudio/build
>  [mm-javac] warning: [options] bootstrap class path not set in
> conjunction with -source 6
>  [mm-javac] error: Source option 6 is no longer supported. Use 7 or later.
>  [mm-javac] error: Target option 6 is no longer supported. Use 7 or later.
>
> BUILD FAILED
> /Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110:
> Compile failed; see the compiler error output for details.
>

What is the error in compiler output?


>
> so my question, what  do you use on mac?
>

JDK1.8.0_191, but I have the feeling that is not the issue.

What is the compiler error?

Did "make fetchdeps" run successfully, and did you run configure afterwards?

Best,

Nico



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Re: MM build on Mac

T1000
In reply to this post by T1000
HI Nico,
where is compiler log located?
 yes.


[ivy:resolve]       /Users/Ravi/mm/3rdpartypublic/classext/DT1.2.jar
[ivy:resolve]     ==== thirdpartynonfree: tried
[ivy:resolve]       -- artifact #DT1.2;!DT1.2.jar:
[ivy:resolve]       /Users/support/mm/3rdparty/classext/DT1.2.jar
[ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:resolve]         ::          UNRESOLVED DEPENDENCIES         ::
[ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:resolve]         :: #ij3d-bin;: not found
[ivy:resolve]         :: #ima3d_;: not found
[ivy:resolve]         :: #DT1.2;: not found
[ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:resolve]
[ivy:resolve] :: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
[ivy:retrieve] :: retrieving :: org.micromanager#micromanager [sync]
[ivy:retrieve]     confs: [build, test, compile, optional, imagej, runtime]
[ivy:retrieve]     0 artifacts copied, 57 already retrieved (0kB/18ms)

BUILD SUCCESSFUL
Total time: 4 seconds


  Build MMCoreJ (MMCore Java wrapper):    yes
   Build MMCorePy (MMCore Python wrapper): yes
   Build Java application (MMStudio):      yes
   Build device adapters:                  yes
   Build closed-source device adapters:    no

   Install MMStudio as ImageJ plugin:      yes
   Target ImageJ directory:                /Users/Ravi/Desktop/ImageJ/
   ij.jar:                                 /Users/Ravi/Desktop/ImageJ//ImageJ.app/Contents/Java/ij.jar
   Install dependency JARs:                yes

First type 'make fetchdeps' once to download Java build dependencies.
Type 'make' to build.
Then type 'make install' to install.



sh-3.2# make | grep "error"
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error: package ome.units does not exist
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:32: error: package ome.units.quantity does not exist
 [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:33: error: package ome.units.quantity does not exist
 [mm-javac] 3 errors

BUILD FAILED
/Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110: Compile failed; see the compiler error output for details.

Total time: 2 seconds
make[1]: *** [MMJ_.jar] Error 1
make: *** [all-recursive] Error 1



BRRavi





> -----Ursprüngliche Nachricht-----
> Von: Stuurman Nico
> Gesendet: Do. 16.05.2019 20:45
> An: Micro-Manager General ,
> Betreff: Re: [micro-manager-general] MM build on Mac
>
> On 5/16/19 11:31 AM, [hidden email] wrote:
>>
>> if I try to build aginst Java jdk-12.0.1.jdk I get following error:
>>
>> Making all in mmstudio
>> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home/
>> /usr/local/bin/ant -Dmm.javacflags="-Xlint:all,-path,-serial" -logger
>> org.apache.tools.ant.listener.SimpleBigProjectLogger jar
>> Buildfile: /Users/support/mm/micro-manager1.4/mmstudio/build.xml
>>
>> mmstudio.compile:
>>  [mm-javac] Compiling 272 source files to
>> /Users/support/mm/micro-manager1.4/mmstudio/build
>>  [mm-javac] warning: [options] bootstrap class path not set in
>> conjunction with -source 6
>>  [mm-javac] error: Source option 6 is no longer supported. Use 7 or later.
>>  [mm-javac] error: Target option 6 is no longer supported. Use 7 or later.
>>
>> BUILD FAILED
>> /Users/support/mm/micro-manager1.4/buildscripts/javabuild.xml:110:
>> Compile failed; see the compiler error output for details.
>>
>
> What is the error in compiler output?
>
>
>>
>> so my question, what  do you use on mac?
>>
>
> JDK1.8.0_191, but I have the feeling that is not the issue.
>
> What is the compiler error?
>
> Did "make fetchdeps" run successfully, and did you run configure afterwards?
>
> Best,
>
> Nico
>
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
>https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> -----Ursprüngliche Nachricht Ende-----










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Re: MM build on Mac

Stuurman, Nico
On 5/16/19 12:09 PM, [hidden email] wrote:

> [ivy:resolve]       /Users/Ravi/mm/3rdpartypublic/classext/DT1.2.jar
> [ivy:resolve]     ==== thirdpartynonfree: tried
> [ivy:resolve]       -- artifact #DT1.2;!DT1.2.jar:
> [ivy:resolve]       /Users/support/mm/3rdparty/classext/DT1.2.jar
> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
> [ivy:resolve]         ::          UNRESOLVED DEPENDENCIES         ::
> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
> [ivy:resolve]         :: #ij3d-bin;: not found
> [ivy:resolve]         :: #ima3d_;: not found
> [ivy:resolve]         :: #DT1.2;: not found
> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
> [ivy:resolve]
> [ivy:resolve] :: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
> [ivy:retrieve] :: retrieving :: org.micromanager#micromanager [sync]
> [ivy:retrieve]     confs: [build, test, compile, optional, imagej, runtime]
> [ivy:retrieve]     0 artifacts copied, 57 already retrieved (0kB/18ms)

Good, Ivy found all dependencies that it can find.

> sh-3.2# make | grep "error"
>   [mm-javac] /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error: package ome.units does not exist

There we go.  The compiler does not find the OME jar package.

Did you re-run configure after make fetchdeps?

Do you have "micromanager1.4/dependencies/artifacts/compile/
ome-xml-5.1.1.jar" (you should, since ivy found it)?

The makefile uses ant to build the source code, and I do not exactly
know what that is doing, and if ant somehow caches dependencies. You can
also try a make clean in the mmstudio directory and then make again.

B.t.w., why do you want to build the 1.4 sources (i.e., why are we
spending time and effort on this)?


Best,

Nico




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Re: MM build on Mac

T1000
In reply to this post by T1000
>        Hi Nico,
I am trying to build in order to adapt the the configure.ac and Makefile.am on Mac.
do thing that is enough to test the makefile only in deviceAdapter?
yes , ome-xml-5.1.1.jar is exsiting..
  yes
  No success.  

Is it possibile any one upload me, a copy of full mm directory where compiling working...So I just need to adap JAVA_HOME  and path to ImageJ



BRRavi

B.t.w., why do you want to build the 1.4 sources (i.e., why are we > spending time and effort on this)?

> -----Ursprüngliche Nachricht-----
> Von: Stuurman Nico
> Gesendet: Do. 16.05.2019 23:12
> An: Micro-Manager General ,
> Betreff: Re: [micro-manager-general] MM build on Mac
>
> On 5/16/19 12:09 PM, [hidden email] wrote:
>> [ivy:resolve]       /Users/Ravi/mm/3rdpartypublic/classext/DT1.2.jar
>> [ivy:resolve]     ==== thirdpartynonfree: tried
>> [ivy:resolve]       -- artifact #DT1.2;!DT1.2.jar:
>> [ivy:resolve]       /Users/support/mm/3rdparty/classext/DT1.2.jar
>> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
>> [ivy:resolve]         ::          UNRESOLVED DEPENDENCIES         ::
>> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
>> [ivy:resolve]         :: #ij3d-bin;: not found
>> [ivy:resolve]         :: #ima3d_;: not found
>> [ivy:resolve]         :: #DT1.2;: not found
>> [ivy:resolve]         ::::::::::::::::::::::::::::::::::::::::::::::
>> [ivy:resolve]
>> [ivy:resolve] :: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
>> [ivy:retrieve] :: retrieving :: org.micromanager#micromanager [sync]
>> [ivy:retrieve]     confs: [build, test, compile, optional, imagej, runtime]
>> [ivy:retrieve]     0 artifacts copied, 57 already retrieved (0kB/18ms)
>
> Good, Ivy found all dependencies that it can find.
>
>> sh-3.2# make | grep "error"
>>   [mm-javac]
> /Users/support/mm/micro-manager1.4/mmstudio/src/org/micromanager/acquisition/OMEMetadata.java:31: error:
> package ome.units does not exist
>
> There we go.  The compiler does not find the OME jar package.
>
> Did you re-run configure after make fetchdeps?
>
> Do you have "micromanager1.4/dependencies/artifacts/compile/
> ome-xml-5.1.1.jar" (you should, since ivy found it)?
>
> The makefile uses ant to build the source code, and I do not exactly
> know what that is doing, and if ant somehow caches dependencies. You can
> also try a make clean in the mmstudio directory and then make again.
>
> B.t.w., why do you want to build the 1.4 sources (i.e., why are we
> spending time and effort on this)?
>
>
> Best,
>
> Nico
>
>
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
>https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> -----Ursprüngliche Nachricht Ende-----










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Re: MM build on Mac

Stuurman, Nico
On 5/16/2019 9:49 PM, [hidden email] wrote:
> I am trying to build in order to adapt the the configure.ac and
> Makefile.am on Mac.

You should not need to have to build the complete Java layer to do so. 
Just make your changes, cd into the directory of your device adapter,
and type make.

> do thing that is enough to test the makefile only in deviceAdapter?
> yes , ome-xml-5.1.1.jar is exsiting..
>    yes
>    No success.

The plot thickens...

I found the same problem on my windows machine.  It turns out that there
is an (old) version of the ome-xml jar in the 3rdpartypublic
repository.  Apparently, when ivy did not find the imagej maven
repository, it used this one to install the ome-xml, and put it in its
cache.  It is now using that (bad) cached version.  You can delete the
cache using:

rm -rf ~/.ivy2/cache/ome/ome-xml

then run make fetchdeps again.  You can check the size of the
ome-xml-5.1.1.jar, it should be different after you did these steps. 
You can also unzip a copy of it and make sure there is a ome/unit
directory in there.

Apparently, all of this is now fixed, but man, what a pain.

Best,

Nico



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Re: MM build on Mac

T1000
In reply to this post by T1000
Hi Nico,
thank you very much for your support.
I am able to build on Mac now....
BRRavi

> -----Ursprüngliche Nachricht-----
> Von: Stuurman Nico
> Gesendet: Fr. 17.05.2019 07:05
> An: Micro-Manager General
>,  , ,  [hidden email]
>,  ,
> Betreff: Re: [micro-manager-general] MM build on Mac
>
> On 5/16/2019 9:49 PM, [hidden email] wrote:
>> I am trying to build in order to adapt the the configure.ac and
>> Makefile.am on Mac.
>
> You should not need to have to build the complete Java layer to do so.  
> Just make your changes, cd into the directory of your device adapter,
> and type make.
>
>> do thing that is enough to test the makefile only in deviceAdapter?
>> yes , ome-xml-5.1.1.jar is exsiting..
>>    yes
>>    No success.
>
> The plot thickens...
>
> I found the same problem on my windows machine.  It turns out that there
> is an (old) version of the ome-xml jar in the 3rdpartypublic
> repository.  Apparently, when ivy did not find the imagej maven
> repository, it used this one to install the ome-xml, and put it in its
> cache.  It is now using that (bad) cached version.  You can delete the
> cache using:
>
> rm -rf ~/.ivy2/cache/ome/ome-xml
>
> then run make fetchdeps again.  You can check the size of the
> ome-xml-5.1.1.jar, it should be different after you did these steps.  
> You can also unzip a copy of it and make sure there is a ome/unit
> directory in there.
>
> Apparently, all of this is now fixed, but man, what a pain.
>
> Best,
>
> Nico
>
>
>
>
> -----Ursprüngliche Nachricht Ende-----










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