BEAST 2 won't execute

[Sal here]

Hi, I've just downloaded BEAST2 on my Mac and it won't launch. I've tried updating Java. I have version 1.8.0_191. Still won't launch.

Thanks

[Remco Bouckaert]

Have you tried the version with Java included, available here: http://www.beast2.org/download-mac-with-jre/ ?

On 5/11/2018, at 3:50 PM, Sal here <scf...@gmail.com> wrote:

Hi, I've just downloaded BEAST2 on my Mac and it won't launch. I've tried updating Java. I have version 1.8.0_191. Still won't launch.

Thanks

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[Sal here]

Hi, Yes. I tried that first and it wouldn't launch. Then tried downloading the jdk file as in here (https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html). Still won't work. Have made sure that it's only version 8 running.

[Remco Bouckaert]

Hi, 

To diagnose the problem, can you try the following: open a terminal and determine the java version by typing:

java -version

It should say something like ‘Java version “1.8.0_191”’. If so, can you type the following in the terminal:

/Applications/BEAST\ 2.5.1/bin/beauti

and let me know what error messages are shown in there terminal.

Cheers,

Remco

[Sal here]

java -version

java version "1.8.0_191"

Java(TM) SE Runtime Environment (build 1.8.0_191-b12)

Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)

/Applications/BEAST\ 2.5.1/bin/beauti

/Applications/BEAST 2.5.1/bin/beauti: line 33: /Applications/BEAST: No such file or directory

[Remco Bouckaert]

On 5/11/2018, at 5:31 PM, Sal here <scf...@gmail.com> wrote:

java -version

java version "1.8.0_191"

Java(TM) SE Runtime Environment (build 1.8.0_191-b12)

Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)

That looks good.

/Applications/BEAST\ 2.5.1/bin/beauti

/Applications/BEAST 2.5.1/bin/beauti: line 33: /Applications/BEAST: No such file or directory

Where did you install BEAST? It usually goes in the Applications folder in ‘BEAST 2.5.1’, so if you installed it elsewhere, can you try

/path/to/BEAST\ 2.5.1/bin/beauti

where you replace ‘/path/to’ the path where you installed BEAST.

Remco

[Sal here]

The BEAST 2.5.1 folder is just in the Applications folder.

If I enter : /Applications/BEAST\ 2.5.1/bin/beauti

I get: /Applications/BEAST 2.5.1/bin/beauti: line 33: /Applications/BEAST: No such file or directory

The files are most definitely in the applications folder and in BEAST2.5.1. I haven't moved anything.

 

[Sal here]

Also if I enter: /Applications/BEAST 2.5.1/bin/beauti

I get: -bash: /Applications/BEAST: No such file or directory

[Remco Bouckaert]

On 5/11/2018, at 7:07 PM, Sal here <scf...@gmail.com> wrote:

Also if I enter: /Applications/BEAST 2.5.1/bin/beauti

I get: -bash: /Applications/BEAST: No such file or directory

That is expected: there is a space in the directory name, which requires a ‘\’-character, otherwise it is interpreted as two separate commands “/Applications/BEAST” and “2.5.1/bin/beauti”, and since “/Applcations/BEAST” is not file this error message appears.

On Monday, November 5, 2018 at 4:33:46 PM UTC+10:30, Sal here wrote:

The BEAST 2.5.1 folder is just in the Applications folder.

If I enter : /Applications/BEAST\ 2.5.1/bin/beauti

I get: /Applications/BEAST 2.5.1/bin/beauti: line 33: /Applications/BEAST: No such file or directory

The files are most definitely in the applications folder and in BEAST2.5.1. I haven't moved anything.

This is more mysterious, since the beauty scripts stops at line 32 and the error indicates something is wrong on line 33. I suppose if you try

cd /Applications/BEAST\ 2.5.1/bin

followed by

./beauti

you get the same error message?

Perhaps you could try

cd /Applications/BEAST\ 2.5.1

followed by

java -cp lib/beast.jar beast.app.beauti.Beauti

which should start BEAUti directory, and see whether an error message appears.

Remco

[Sal here]

It worked!

When I tried this, the application Beauti launched.:

[Sal here]

The second option also launched Beuti. ie.

[Remco Bouckaert]

Thanks for all the information — starting BEAUti from the script instead of using java allows loading other packages, so that is the preferred option. Unfortunately, it does not explain why BEAUti does not launch through other ways...

If you cannot start BEAST through the icon under Applications, to start BEAST, you probably need to do

cd /Applications/BEAST\ 2.5.1\bin

followed by

./beast

Just one more question: which version of OS X are you using? Perhaps it is some security setting that prevents BEAUti from starting in the usual way, and those settings can change with different OS X versions.

Cheers,

Remco

[Sal here]

Thanks so much for your help. Much appreciated.

I'm using Mojave 10.14.

Cheers,

Sally

[Remco Bouckaert]

Hi Sally,

Thanks for letting me know. I’ll investigate whether it is something that changed in Mojave.

Cheers, Remco