Opening anTrax issue

[MarkJThomas]

Hi,
thank you for the app!
I tried opening the app but kept getting the below error: (I am on Mac OS)

First, I downloaded tensorflow version 1.15 in the conda env tf15 and successfully installed anTrax:

(base) markthomas@Marks-Air anTrax % conda activate tf15

Next, I tried running the code as per the instructions:

(tf15) markthomas@Marks-Air anTrax % antrax configure /Users/markthomas/Desktop/Home/MRes/Other_chapters/Ants/anTraX/anTraX-data/JS16

But got this error:

Traceback (most recent call last):
File "/Users/markthomas/miniconda3/envs/tf15/bin/antrax", line 5, in
from antrax.cli import main
File "/Users/markthomas/miniconda3/envs/tf15/lib/python3.7/site-packages/antrax/cli.py", line 5, in
from .matlab import *
File "/Users/markthomas/miniconda3/envs/tf15/lib/python3.7/site-packages/antrax/matlab.py", line 22, in
ANTRAX_BIN_PATH = ANTRAX_PATH + '/bin/'
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

Any help is greatly appreciated!

[MarkJThomas]

I think it's related to MATLAB reading the code, and I thought I had it installed but maybe that is the reason?
tyi

[asafgal]

Hey Mark, thanks for trying out anTraX! Did you set the ANTRAX_PATH environment variable? Make sure it is available within your conda environment.

…

On 1 Nov 2021, at 13:45, MarkJThomas ***@***.***> wrote: I think it's related to MATLAB reading the code, and I thought I had it installed but maybe that is the reason? tyi — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACERP5VVG4E5RQI43YKKG4TUJZ4VBANCNFSM5HD2D4CA>.

[MarkJThomas]

I didn't, I am not technically sound - do you have/or point me in the direction of how I can do that please?

[asafgal]

See in the installation instructions:

export ANTRAX_PATH=<full path to anTraX repository>
export ANTRAX_USE_MCR=False

You can verify the variables by typing in terminal while inside the conda environment:

echo $ANTRAX_PATH

[MarkJThomas]

ty, can I just confirm I need to install MATLAB?

[asafgal]

Yes, you need either MATLAB or MCR installed. If you have a MATLAB license, it is better to install it rather than using MCR.

…

On 1 Nov 2021, at 14:13, MarkJThomas ***@***.***> wrote: ty, can I just confirm I need to install MATLAB? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#32 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACERP5XFQWVEZWYJJDSORTLUJ2AABANCNFSM5HD2D4CA>.

[MarkJThomas]

I don't have any of them installed or a MATLAB license - do you download it here (MCR): https://uk.mathworks.com/products/compiler/matlab-runtime.html

Please forgive all the questions! This is quite new to me :)

[asafgal]

Yes, choose version R2019a.

Don't worry about it! hope it will work out for you

[MarkJThomas]

Thank you for your support! I managed to get MATLAB installed and connect the paths, and it says Welcome to AnTrax, however, I get this error now:

dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
Referenced from: /Users/markthomas/Desktop/Home/MRes/Other_chapters/Ants/anTraX/bin/antrax_maci64_mcr_interface.app/Contents/MacOS/antrax_maci64_mcr_interface
Reason: image not found

Do you know what that is referring too?

tyi

[asafgal]

Hey Mark, sorry for the delayed reply.

You also need to define the path to MCR (I'm guessing that what you use):

export ANTRAX_MCR=<full path to MCR installation>

Try to follow the installation steps in the docs!

[MarkJThomas]

Thank you! I did but I didn't know which folder to define the path too, there's a lot of different ones. When I added the path to the main folder nothing opened, then when I defined it to the current folder it opens but I get the above error message. These are the paths currently loaded in my .zprofile:

[asafgal]

The path should be to v96 directory

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On 4 Nov 2021, at 17:23, MarkJThomas ***@***.***> wrote: Thank you! I did but I didn't know which folder to define the path too, there's a lot of different ones. When I added the path to the main folder nothing opened, then when I defined it to the current folder it opens but I get the above error message. These are the paths currently loaded in my .zprofile: <https://user-images.githubusercontent.com/41441629/140349977-1e6c7581-11af-4892-905b-90c083c57bb2.png> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#32 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACERP5UD5WBG44ISXMNNAYLUKKQONANCNFSM5HD2D4CA>.

[MarkJThomas]

updated but just got the same error message:

dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
Referenced from: /Users/markthomas/Desktop/Home/MRes/Other_chapters/Ants/anTraX/bin/antrax_maci64_mcr_interface.app/Contents/MacOS/antrax_maci64_mcr_interface
Reason: image not found
(tf15) markthomas@Marks-Air ~ %

Maybe it's just not meant to be :D

[janamach]

I just installed anTraX on a new work computer running Ubuntu 20.04. I had anTraX working on multiple other machines, so I just copied all my config files as I usually do (which usually works). But not this time. For whatever reason I got this error message:

$ antrax configure 

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

02/03/22 21:12:54 -D- antrax cli entry point
02/03/22 21:12:54 -D- running matlab mcr 
02/03/22 21:12:54 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface antrax
/home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface: error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory
02/03/22 21:12:54 -D- matlab app exited with code 127

A quick search for libmwlaunchermain lead me to your post, @MarkJThomas. On my system, something weird has happened and the library was not loading even though the correct LD_LIBRARY_PATH was set.

A similar issue is discussed here:
https://mathworks.com/matlabcentral/answers/267562-how-can-i-resolve-this-mcc-runtime-error-cannot-open-shared-object-library#answer_211306
And I found my "solution" here:
https://mathworks.com/help/compiler/mcr-path-settings-for-run-time-deployment.html

The "solution" I found is bizarre, but it works for some reason:

LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Runtime/v96/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/extern/bin/glnxa64

mypath=$LD_LIBRARY_PATH
mypath="${mypath:+${mypath}:}"
export LD_LIBRARY_PATH=$mypath

And then antrax loads normally:

$ antrax configure

==================================================================================

Welcome to anTraX - a software for tracking color tagged ants (and other insects)

==================================================================================

02/03/22 21:47:08 -D- antrax cli entry point
02/03/22 21:47:08 -D- running matlab mcr 
02/03/22 21:47:08 -D- command is: /home/jana/src/anTraX/bin/antrax_glnxa64_mcr_interface antrax
21:47:14 -D- starting antrax configure app
app closing..
02/03/22 21:47:20 -D- matlab app exited with code 0

While doing simply this LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}" doesn't help. And the above "solution" makes little sense, because LD_LIBRARY_PATH barely changes after the procedure:

$ echo ${LD_LIBRARY_PATH}
/usr/local/MATLAB/MATLAB_Runtime/v96/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v96/extern/bin/glnxa64::

I really don't understand this, it's very weird... Anyhow, I am writing this here in case somebody else runs into this problem.

@MarkJThomas looking at your post, I think you should try following the steps in the link I posted above for macOS. If it's a library not found thing, it should be fixable.