beauti 2.6.7 was working perfectly but after updating packages via beauti package manager is not working anymore

[Jovana Jasso]

Hello everyone,

I have been using beauti 2.6.7 for making .xml files for dating analyses. I already run these files in BEAST and after checking the results I wanted to make modifications and provide a Simple Constraint Random Tree; however, when I selected this option no more options were displayed (see pic below). 

I thought that by updating packages via the beauti package manager it would be fixed but it went even worse since now beauti is not working anymore; when I try to open it i get many emerging windows with messages like "package xx needs package xx which is not available".

Then I uninstalled and installed beast/beauti 2.6.7 again but the same problem remain. I also tried with beast/beauti v. 2.6.6, 2.6.5, etc. but the same. Weird because i also have the version 2.7.6 and it is working perfectly; however, since I made my files in a previous version, I cannot edit them in the 2.7 one. 

I then tried to open beauti from the terminal, but the same.

Probably a java problem? Have any of you get similar errors?

Below more information that could be useful.

Thanks!

java info:

jovana$ java -version

java version "1.8.0_401"

Java(TM) SE Runtime Environment (build 1.8.0_401-b10)

Java HotSpot(TM) 64-Bit Server VM (build 25.401-b10, mixed mode)

beauti error when tried to open it from the terminal (same as when I tried to open bi clicking): 

jovana$ /Applications/BEAST_2.6.7/bin/beauti

Package BDMM requires another package (SA) which is not available.

Either uninstall BDMM or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package speedemon requires another package (BICEPS) which is not available.

Either uninstall speedemon or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package contraband requires another package (SA) which is not available.

Either uninstall contraband or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package starbeast2 requires another package (SA) which is not available.

Either uninstall starbeast2 or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package contraband requires another package (MM) which is not available.

Either uninstall contraband or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package speedemon requires another package (snapper) which is not available.

Either uninstall speedemon or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package speedemon requires another package (starbeast3) which is not available.

Either uninstall speedemon or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package lphybeast requires another package (feast) which is not available.

Either uninstall lphybeast or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Package starbeast2 requires another package (MM) which is not available.

Either uninstall starbeast2 or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

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beauticonfig

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run

java.lang.IllegalArgumentException: biceps/YuleSkyline

at beast.app.beauti.BeautiSubTemplate.initAndValidate(Unknown Source)

at beast.util.XMLParser.initBEASTObjects(Unknown Source)

at beast.util.XMLParser.parseTemplate(Unknown Source)

at beast.app.beauti.BeautiDoc.loadTemplate(Unknown Source)

at beast.app.beauti.BeautiDoc.mergeSequences(Unknown Source)

at beast.app.beauti.BeautiDoc.initialize(Unknown Source)

at beast.app.beauti.BeautiDoc.parseArgs(Unknown Source)

at beast.app.beauti.Beauti.main2(Unknown Source)

at beast.app.beauti.Beauti.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beauti.BeautiLauncher.main(Unknown Source)

beast.util.XMLParserException: 

Error 110 parsing the xml input file

validate and intialize error: biceps/YuleSkyline

Error detected about here:

  <beast>

      <beauticonfig spec='BeautiConfig'>

          <subtemplate id='YuleSkylineCollapse'>

at beast.util.XMLParser.initBEASTObjects(Unknown Source)

at beast.util.XMLParser.parseTemplate(Unknown Source)

at beast.app.beauti.BeautiDoc.loadTemplate(Unknown Source)

at beast.app.beauti.BeautiDoc.mergeSequences(Unknown Source)

at beast.app.beauti.BeautiDoc.initialize(Unknown Source)

at beast.app.beauti.BeautiDoc.parseArgs(Unknown Source)

at beast.app.beauti.Beauti.main2(Unknown Source)

at beast.app.beauti.Beauti.main(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beauti.BeautiLauncher.main(Unknown Source)