installation help

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installation help

Callaway, Anton
I am trying to install Micromanager on an Ubuntu Lite 3.6, version 16.04, xenial box.
Installation fails at the "make fetchdeps" step with an error message something like:
make: no target 'fetchdeps'. Stop.
Reading past posts from people having similar problems, it seemed that it might be a problem with Java.
I have javac version 1.8.0_181.

Any help would be greatly appreciated.
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus


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Re: installation help

Kyle Douglass-2
Hi Anton,
Did you run the `autogen.sh` and `configure` scripts before `make fetchdeps`? Did they succeed or fail?

The error is telling you that there is no rule for `fetchdeps` in the Makefile. For example, when you run `make install` there is an explicit  rule defined in the Makefile named `install` that contains the steps that should be carried out to install the software. These steps are usually, but not always, shell commands. More specifically, the error message means that either the rule is not present in the Makefile, or one of these two prior steps did not create the Makefile.

As a sanity check, can you verify that the Makefile is present and, if yes, open it with a text editor to check that there is a `fetchdeps` rule?

If the `configure` script succeeded, pay close attention to its output. It will tell you whether it detected Java on your system. If it did not, then make will skip building the Java components, which is another possibility for why the rule could be missing. When I build the MM core and Python wrappers, I explicitly disable Java in the call to `configure` and do not run `make fetchdeps` at all, so it is not a required step if you don't build the Java components.

Finally, if it didn't detect Java, you can manually configure it by changing the arguments to the configure script. To see what these are, try running `./configure --help`. (I am going by memory and might be wrong about the specifics, but the help menu definitely exists and I have used it before to create highly customized MM Linux builds; see http://kmdouglass.github.io/posts/micro-manager-on-the-raspberry-pi.html for example.)

Write back if you make any progress, and good luck!
Kyle

On Thu, Nov 8, 2018, 18:54 Callaway, Anton <[hidden email] wrote:
I am trying to install Micromanager on an Ubuntu Lite 3.6, version 16.04, xenial box.
Installation fails at the "make fetchdeps" step with an error message something like:
make: no target 'fetchdeps'. Stop.
Reading past posts from people having similar problems, it seemed that it might be a problem with Java.
I have javac version 1.8.0_181.

Any help would be greatly appreciated.
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: installation help

Callaway, Anton
Kyle,

Thank you for your response!
I took a closer look at the output and it seems that the install of ImageJ (or rather the lack thereof) may be the problem.  I'm not sure if I have the wrong JVM or if it is the ImageJ installation itself that is at fault.

I've attached dumps from the shell, if you have time to take a look.
Best regards,
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus

________________________________________
From: Kyle Douglass [[hidden email]]
Sent: Thursday, November 08, 2018 10:53 AM
To: Micro-Manager General
Subject: Re: [micro-manager-general] installation help

Hi Anton,
Did you run the `autogen.sh` and `configure` scripts before `make fetchdeps`? Did they succeed or fail?

The error is telling you that there is no rule for `fetchdeps` in the Makefile. For example, when you run `make install` there is an explicit  rule defined in the Makefile named `install` that contains the steps that should be carried out to install the software. These steps are usually, but not always, shell commands. More specifically, the error message means that either the rule is not present in the Makefile, or one of these two prior steps did not create the Makefile.

As a sanity check, can you verify that the Makefile is present and, if yes, open it with a text editor to check that there is a `fetchdeps` rule?

If the `configure` script succeeded, pay close attention to its output. It will tell you whether it detected Java on your system. If it did not, then make will skip building the Java components, which is another possibility for why the rule could be missing. When I build the MM core and Python wrappers, I explicitly disable Java in the call to `configure` and do not run `make fetchdeps` at all, so it is not a required step if you don't build the Java components.

Finally, if it didn't detect Java, you can manually configure it by changing the arguments to the configure script. To see what these are, try running `./configure --help`. (I am going by memory and might be wrong about the specifics, but the help menu definitely exists and I have used it before to create highly customized MM Linux builds; see http://kmdouglass.github.io/posts/micro-manager-on-the-raspberry-pi.html for example.)

Write back if you make any progress, and good luck!
Kyle

On Thu, Nov 8, 2018, 18:54 Callaway, Anton <[hidden email]<mailto:[hidden email]> wrote:
I am trying to install Micromanager on an Ubuntu Lite 3.6, version 16.04, xenial box.
Installation fails at the "make fetchdeps" step with an error message something like:
make: no target 'fetchdeps'. Stop.
Reading past posts from people having similar problems, it seemed that it might be a problem with Java.
I have javac version 1.8.0_181.

Any help would be greatly appreciated.
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus
_______________________________________________
micro-manager-general mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

MMInstall_shellDumps.txt (14K) Download Attachment
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Re: installation help

Kyle Douglass-2
Hi Anton,
I took a quick look at the logs and you are indeed right that the Micro-Manager configuration script fails because it cannot find the ImageJ jar. This may be fixed by doing exactly what the log says: specify the location to the jar with the `--with-ij-jar=FILE` flag to the configure script, replacing FILE with the full path to the jar. Try searching for ij.jar on your syate.

The second problem as you are no doubt aware is that ImageJ doesn't appear to run on your system.

Can you please tell me how you installed ImageJ including where you got it from?

If you have some time to play with it, I would also try different a different JDK version and/or the Oracle JDK instead of OpenJDK. Both Oracle JDK 8 and OpenJDK 8 should work.

Cheers,
Kyle

On Nov 21, 2018 01:12, "Callaway, Anton" <[hidden email]> wrote:
Kyle,

Thank you for your response!
I took a closer look at the output and it seems that the install of ImageJ (or rather the lack thereof) may be the problem.  I'm not sure if I have the wrong JVM or if it is the ImageJ installation itself that is at fault.

I've attached dumps from the shell, if you have time to take a look.
Best regards,
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus

________________________________________
From: Kyle Douglass [[hidden email]]
Sent: Thursday, November 08, 2018 10:53 AM
To: Micro-Manager General
Subject: Re: [micro-manager-general] installation help

Hi Anton,
Did you run the `autogen.sh` and `configure` scripts before `make fetchdeps`? Did they succeed or fail?

The error is telling you that there is no rule for `fetchdeps` in the Makefile. For example, when you run `make install` there is an explicit  rule defined in the Makefile named `install` that contains the steps that should be carried out to install the software. These steps are usually, but not always, shell commands. More specifically, the error message means that either the rule is not present in the Makefile, or one of these two prior steps did not create the Makefile.

As a sanity check, can you verify that the Makefile is present and, if yes, open it with a text editor to check that there is a `fetchdeps` rule?

If the `configure` script succeeded, pay close attention to its output. It will tell you whether it detected Java on your system. If it did not, then make will skip building the Java components, which is another possibility for why the rule could be missing. When I build the MM core and Python wrappers, I explicitly disable Java in the call to `configure` and do not run `make fetchdeps` at all, so it is not a required step if you don't build the Java components.

Finally, if it didn't detect Java, you can manually configure it by changing the arguments to the configure script. To see what these are, try running `./configure --help`. (I am going by memory and might be wrong about the specifics, but the help menu definitely exists and I have used it before to create highly customized MM Linux builds; see http://kmdouglass.github.io/posts/micro-manager-on-the-raspberry-pi.html for example.)

Write back if you make any progress, and good luck!
Kyle

On Thu, Nov 8, 2018, 18:54 Callaway, Anton <[hidden email]<mailto:[hidden email]> wrote:
I am trying to install Micromanager on an Ubuntu Lite 3.6, version 16.04, xenial box.
Installation fails at the "make fetchdeps" step with an error message something like:
make: no target 'fetchdeps'. Stop.
Reading past posts from people having similar problems, it seemed that it might be a problem with Java.
I have javac version 1.8.0_181.

Any help would be greatly appreciated.
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus
_______________________________________________
micro-manager-general mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general



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Re: installation help

Callaway, Anton
Thanks for your response, Kyle.

I got ImageJ from the official Linux Lite repository and installed it as per the usual process for installing apps on this platform ("Install/Remove Software" in the GUI).  I tried completely removing the software (again with the GUI) and re-installing.  Then I got pulled away with other responsibilities and didn't go back and try installing via command line.  What do you recommend? 

I will try the Oracle JDK ASAP.

Best regards,

Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus

From: Kyle Douglass [[hidden email]]
Sent: Saturday, November 24, 2018 6:28 AM
To: Micro-Manager General
Subject: Re: [micro-manager-general] installation help

Hi Anton,
I took a quick look at the logs and you are indeed right that the Micro-Manager configuration script fails because it cannot find the ImageJ jar. This may be fixed by doing exactly what the log says: specify the location to the jar with the `--with-ij-jar=FILE` flag to the configure script, replacing FILE with the full path to the jar. Try searching for ij.jar on your syate.

The second problem as you are no doubt aware is that ImageJ doesn't appear to run on your system.

Can you please tell me how you installed ImageJ including where you got it from?

If you have some time to play with it, I would also try different a different JDK version and/or the Oracle JDK instead of OpenJDK. Both Oracle JDK 8 and OpenJDK 8 should work.

Cheers,
Kyle

On Nov 21, 2018 01:12, "Callaway, Anton" <[hidden email]> wrote:
Kyle,

Thank you for your response!
I took a closer look at the output and it seems that the install of ImageJ (or rather the lack thereof) may be the problem.  I'm not sure if I have the wrong JVM or if it is the ImageJ installation itself that is at fault.

I've attached dumps from the shell, if you have time to take a look.
Best regards,
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus

________________________________________
From: Kyle Douglass [[hidden email]]
Sent: Thursday, November 08, 2018 10:53 AM
To: Micro-Manager General
Subject: Re: [micro-manager-general] installation help

Hi Anton,
Did you run the `autogen.sh` and `configure` scripts before `make fetchdeps`? Did they succeed or fail?

The error is telling you that there is no rule for `fetchdeps` in the Makefile. For example, when you run `make install` there is an explicit  rule defined in the Makefile named `install` that contains the steps that should be carried out to install the software. These steps are usually, but not always, shell commands. More specifically, the error message means that either the rule is not present in the Makefile, or one of these two prior steps did not create the Makefile.

As a sanity check, can you verify that the Makefile is present and, if yes, open it with a text editor to check that there is a `fetchdeps` rule?

If the `configure` script succeeded, pay close attention to its output. It will tell you whether it detected Java on your system. If it did not, then make will skip building the Java components, which is another possibility for why the rule could be missing. When I build the MM core and Python wrappers, I explicitly disable Java in the call to `configure` and do not run `make fetchdeps` at all, so it is not a required step if you don't build the Java components.

Finally, if it didn't detect Java, you can manually configure it by changing the arguments to the configure script. To see what these are, try running `./configure --help`. (I am going by memory and might be wrong about the specifics, but the help menu definitely exists and I have used it before to create highly customized MM Linux builds; see http://kmdouglass.github.io/posts/micro-manager-on-the-raspberry-pi.html for example.)

Write back if you make any progress, and good luck!
Kyle

On Thu, Nov 8, 2018, 18:54 Callaway, Anton <[hidden email]<mailto:[hidden email]> wrote:
I am trying to install Micromanager on an Ubuntu Lite 3.6, version 16.04, xenial box.
Installation fails at the "make fetchdeps" step with an error message something like:
make: no target 'fetchdeps'. Stop.
Reading past posts from people having similar problems, it seemed that it might be a problem with Java.
I have javac version 1.8.0_181.

Any help would be greatly appreciated.
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus
_______________________________________________
micro-manager-general mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general



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Re: installation help

Kyle Douglass-2
Hi Anton,

On Mon, Nov 26, 2018 at 6:10 PM Callaway, Anton <[hidden email]> wrote:

I got ImageJ from the official Linux Lite repository and installed it as per the usual process for installing apps on this platform ("Install/Remove Software" in the GUI).  I tried completely removing the software (again with the GUI) and re-installing.  Then I got pulled away with other responsibilities and didn't go back and try installing via command line.  What do you recommend? 


I would try the following:
1. Assuming Java is correctly installed, download the Platform Independent version of ImageJ (not FIJI) from the ImageJ NIH website: https://imagej.nih.gov/ij/download.html
2. Unzip it to a directory of your choosing
3. On the command line, run the Micromanager configure script, setting the --with-ij-jar=path/to/ij.jar flag when running the script. (See my earlier response for more info)

./configure --with-ij-jar=path/to/ij.jar

Then try running make fetchdeps, etc...

You might be able to use the versions of ImageJ from the NIH website with Java installed, but then you will need to pass additional flags to the configure script to setup Java.

Cheers,
Kyle


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Re: installation help

Callaway, Anton
Thanks again for your response and patience, Kyle.

I downloaded the PI version of ImageJ, installed it, etc. as instructed.  I am still getting fatal Java errors just trying to run IJ and the make fetchdeps command still returns the same error (see new shell dumps attached).

I completely removed the previous IJ installed through the Linux Lite repository to help ensure a clean new install and I checked the Makefile and verified that there are fetchdeps instructions.  This is already some progress, because I don't think I was even getting a Makefile generated before.
Thanks,
Anton

Anton Callaway, PhD
Gibson Lab
University of British Columbia, Okanagan campus
________________________________
From: Kyle Douglass [[hidden email]]
Sent: Monday, November 26, 2018 9:49 PM
To: Micro-Manager General
Subject: Re: [micro-manager-general] installation help

Hi Anton,

On Mon, Nov 26, 2018 at 6:10 PM Callaway, Anton <[hidden email]<mailto:[hidden email]>> wrote:

I got ImageJ from the official Linux Lite repository and installed it as per the usual process for installing apps on this platform ("Install/Remove Software" in the GUI).  I tried completely removing the software (again with the GUI) and re-installing.  Then I got pulled away with other responsibilities and didn't go back and try installing via command line.  What do you recommend?


I would try the following:
1. Assuming Java is correctly installed, download the Platform Independent version of ImageJ (not FIJI) from the ImageJ NIH website: https://imagej.nih.gov/ij/download.html
2. Unzip it to a directory of your choosing
3. On the command line, run the Micromanager configure script, setting the --with-ij-jar=path/to/ij.jar flag when running the script. (See my earlier response for more info)

./configure --with-ij-jar=path/to/ij.jar

Then try running make fetchdeps, etc...

You might be able to use the versions of ImageJ from the NIH website with Java installed, but then you will need to pass additional flags to the configure script to setup Java.

Cheers,
Kyle


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micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

NewImageJScreenDumps.txt (63K) Download Attachment