BEAST related error

[thijsjanzen]

Upon running mcbette::est_marg_liks:

mcbette::est_marg_liks(fasta_filename = "rag1_trimal.fasta")

I receive the following error:

Error: Could not find or load main class beast.util.PackageManager
Error: mauricer::is_beast2_pkg_installed("NS") are not all TRUE
In addition: Warning message:
In system2(command = beastier::get_default_java_path(), args = c("-cp",  :
  running command ''/Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre/bin/java' -cp '/Users/janzen/Library/Application Support/BEAST/lib/beast.jar' beast.util.PackageManager -list' had status 1

[thijsjanzen]

Upon running mcbette::est_marg_liks:

mcbette::est_marg_liks(fasta_filename = "rag1_trimal.fasta")

I receive the following error:

Error: Could not find or load main class beast.util.PackageManager
Error: mauricer::is_beast2_pkg_installed("NS") are not all TRUE
In addition: Warning message:
In system2(command = beastier::get_default_java_path(), args = c("-cp",  :
  running command ''/Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre/bin/java' -cp '/Users/janzen/Library/Application Support/BEAST/lib/beast.jar' beast.util.PackageManager -list' had status 1

I suspect it has something to do with the installation folders of BEAST and/or Java...
I have tried installing BEAST using beastier, but this gives the report that BEAST is already installed (which is correct).
Alternatively, I have used beastier to install beast in a custom folder, but in mcbette I can not specify the path of BEAST.

[richelbilderbeek]

Thanks for this Issue!

This is not a mcbette error: Travis proves mcbette works on such a simple example.

Instead, the error was at my side, as I hadn't put any installation instructions anywhere. They are here. Do that on a UNIX machine and it should work. If not, go ahead and create a new Issues 👍

Closing this one now, feel free to re-open iff there are questions about my answer 🌈

[thijsjanzen]

I'm afraid that doesn't solve the issue, upon mauricer::install_beast2_pkg("NS") I receive:

Error: Could not find or load main class beast.util.PackageManager
Error in if (is_beast2_pkg_installed(name)) { : 
  argument is of length zero
In addition: Warning message:
In system2(command = beastier::get_default_java_path(), args = c("-cp",  :
  running command ''/Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre/bin/java' -cp '/Users/janzen/Library/Application Support/BEAST/lib/beast.jar' beast.util.PackageManager -list' had status 1

(also, interestingly from the installation instructions, the line 'devtools::install_github("richelbilderbeek/mcbette") is missing ;) )

[richelbilderbeek]

Hmmm, I see I do not build mcbette under macOS. Add this to the test and running it now . I'll keep you posted.

Fixed the doc 👍

[thijsjanzen]

Still doesn't work... also, your travis run crashed as well it appears:

mauricer::install_beast2_pkg("NS")

Error: Could not find or load main class beast.util.PackageManager
Error in if (is_beast2_pkg_installed(name)) { : 
  argument is of length zero
In addition: Warning message:
In system2(command = beastier::get_default_java_path(), args = c("-cp",  :
  running command ''/Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre/bin/java' -cp '/Users/janzen/Library/Application Support/BEAST/lib/beast.jar' beast.util.PackageManager -list' had status 1

mcbette::est_marg_liks(fasta_filename = "test.fasta")

Error: Could not find or load main class beast.util.PackageManager
Error: mauricer::is_beast2_pkg_installed("NS") are not all TRUE
In addition: Warning message:
In system2(command = beastier::get_default_java_path(), args = c("-cp",  :
  running command ''/Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre/bin/java' -cp '/Users/janzen/Library/Application Support/BEAST/lib/beast.jar' beast.util.PackageManager -list' had status 1

[richelbilderbeek]

Both Travis builds work fine: develop, 164 and master, 154.

I wonder if it has to do with the spaces in your path to BEAST2, /Users/janzen/Library/Application Support/BEAST/lib/beast.jar. Is the the default location beastier installs BEAST2 to?