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Wix pre-processor rejecting class files with `$anon$` in them from a Scala application

I'm trying to automate the build process of my Scala application for producing a msi installer.
When doing so, windows claims that certain files cannot be found. Here is the command that gets run
[21:39:01.842] Running C:\Program Files (x86)\WiX Toolset v3.11\bin\candle.exe in C:\Users\RUNNER~1\AppData\Local\Temp\jdk.jpackage6105194214114584024\images\win-msi.image\krystalbull
and further down, i start seeing errors like this:
C:\Users\runneradmin\AppData\Local\Temp\jdk.jpackage6105194214114584024\config\bundle.wxf(56) : error LGHT0103 : The system cannot find the file 'C:\Users\RUNNER~1\AppData\Local\Temp\jdk.jpackage6105194214114584024\images\win-msi.image\krystalbull\app\classes\com\krystal\bull\gui\FileMenu$anon$2.class'.
C:\Users\runneradmin\AppData\Local\Temp\jdk.jpackage6105194214114584024\config\bundle.wxf(71) : error LGHT0103 : The system cannot find the file 'C:\Users\RUNNER~1\AppData\Local\Temp\jdk.jpackage6105194214114584024\images\win-msi.image\krystalbull\app\classes\com\krystal\bull\gui\dialog\ViewEventDialog$anon$10$anon$21$anonfun$lessinit$greater$1.class'.
C:\Users\runneradmin\AppData\Local\Temp\jdk.jpackage6105194214114584024\config\bundle.wxf(81) : error LGHT0103 : The system cannot find the file 'C:\Users\RUNNER~1\AppData\Local\Temp\jdk.jpackage6105194214114584024\images\win-msi.image\krystalbull\app\classes\com\krystal\bull\gui\SettingsMenu$anon$5.class'.
You can see more instances of this error in the build log here:
https://github.com/bitcoin-s/krystal-bull/runs/2697961906?check_suite_focus=true#step:8:11
My question is this:
What are the limitations in the windows file system or the program candle.exe that prevent the pre-processor from reading Scala files that include things like $anon$
Is there a valid syntax guide somewhere?
Will I need to manually rename all of these files?

Matlab installation (LD_LIBRARY_PATH) messes up other library files

I am trying to install Matlab on a Linux machine, but setting LD_LIBRARY_PATH (as the installation requires) breaks other library files. I am not an Linux expert, but I have tried several things and cannot get it working correctly. I have even contacted Matlab support, got the issue elevated to the dev team, and was basically told "haha sucks to suck". I have seen a few other people online have had the same issue, but either their questions were never answered or they had a slightly different problem and their solution didn't apply to me.
Installing on a VM running Ubuntu:
I set LD_LIBRARY_PATH as the instructions say, then it breaks network files. I can ping google.com, but I cannot nslookup google.com or visit it in a browser. Nslookup provides this error:
nslookup: /usr/local/MATLAB/MATLAB_Runtime/v90/bin/glnxa64/libcrypto.so.1.0.0: no version information available (required by /usr/lib/libdns.so.100)
03-Feb-2016 11:32:22.361 ENGINE_by_id failed (crypto failure)
03-Feb-2016 11:32:22.362 error:25070067:DSO support routines:DSO_load:could not load the shared library:dso_lib.c:244:
03-Feb-2016 11:32:22.363 error:260B6084:engine routines:DYNAMIC_LOAD:dso not found:eng_dyn.c:447:
03-Feb-2016 11:32:22.363 error:2606A074:engine routines:ENGINE_by_id:no such engine:eng_list.c:418:id=gost
(null): dst_lib_init: crypto failure
The installation worked though (I can run my Java programs that reference compiled Matlab functions). Unsetting LD_LIBRARY_PATH fixes the network files but then I can't run programs anymore.
Installing on EC2 instance:
On an EC2 instance it does not break the network files (nslookup is fine). Instead it messes up Python library files. Trying to use any aws cli command, I get the error:
File "/usr/bin/aws", line 19, in <module>
import awscli.clidriver
File "/usr/lib/python2.7/dist-packages/awscli/clidriver.py", line 16, in <module>
import botocore.session
File "/usr/lib/python2.7/dist-packages/botocore/session.py", line 25, in <module>
import botocore.config
File "/usr/lib/python2.7/dist-packages/botocore/config.py", line 18, in <module>
from botocore.compat import six
File "/usr/lib/python2.7/dist-packages/botocore/compat.py", line 139, in <module>
import xml.etree.cElementTree
File "/usr/lib64/python2.7/xml/etree/cElementTree.py", line 3, in <module>
from _elementtree import *
ImportError: PyCapsule_Import could not import module "pyexpat"
Printing sys.path in Python shows lib-dynload is already there though, so it doesn't seem to the problem.
And when trying to run the program, I get:
Exception in thread "main" java.lang.LinkageError: libXt.so.6: cannot open shared object file: No such file or directory
at com.mathworks.toolbox.javabuilder.internal.DynamicLibraryUtils.dlopen(Native Method)
at com.mathworks.toolbox.javabuilder.internal.DynamicLibraryUtils.loadLibraryAndBindNativeMethods(DynamicLibraryUtils.java:134)
at com.mathworks.toolbox.javabuilder.internal.MWMCR.<clinit>(MWMCR.java:1529)
at VectorAddExample.VectorAddExampleMCRFactory.newInstance(VectorAddExampleMCRFactory.java:48)
at VectorAddExample.VectorAddExampleMCRFactory.newInstance(VectorAddExampleMCRFactory.java:59)
at VectorAddExample.VectorAddClass.<init>(VectorAddClass.java:62)
at com.mypackage.Example.main(Example.java:13)
I'm at a brick wall and really have no clue how to proceed.

Maybe something else already needs LD_LIBRARY_PATH set to work. Make sure you prepend not overwrite:
export LD_LIBRARY_PATH=new/path:$LD_LIBRARY_PATH
Edit:
OK, if LD_LIBRARY_PATH was initially empty, this suggests that Matlab comes with shared libraries that are incompatible with your system ones:
nslookup: /usr/local/MATLAB/MATLAB_Runtime/v90/bin/glnxa64/libcrypto.so.1.0.0: no version information available (required by /usr/lib/libdns.so.100)
suggests that /usr/lib/libdns.so.100 needs libcrypto.so.1.0.0, which is now being resolved to the one that comes with MATLAB, which is incompatible.
You can check the dependencies of a dll by
ldd /usr/lib/libcrypto.so.1.0.0
and hopefully you can find a configuration that keeps both MATLAB and your system happy. Unfortunately, this may involve a lot of trial and error.
If there is no such configuration, you can try setting LD_LIBRARY_PATH only when you run MATLAB:
LD_LIBRARY_PATH=$MATLAB_LD_LIBRARY_PATH matlab
Edit 2:
Well, for the Python issue, it seems to boil down to pyexpat, which is a wrapper around the standard expat XML parser. Try doing (name guessed since I don't have a Linux right now):
ldd /usr/local/lib/python2.7/site-packages/libpyexpat.so
and see what that depends on. Probably, it will be libexpat.so, which is now being resolved to MATLAB's version.

try the following command:
export LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Runtime/v90/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v90/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v90/sys/os‌​/glnxa64:$LD_LIBRARY_PATH

Perhaps not helpful for OP but if you are generating a python package with MATLAB, you could modify the generated __init__.py file MATLAB creates for your package.
Specifically, the generated __init__.py file contains the following line (as of MATLAB 2017a):
PLATFORM_DICT = {'Windows': ['PATH','dll',''], 'Linux': ['LD_LIBRARY_PATH','so','libmw'], 'Darwin': ['DYMCR_LIBRARY_PATH','dylib','libmw']}
For Linux platform, you could simply replace LD_LIBRARY_PATH with something else such as MCR_LIBRARY_PATH to prevent mucking with your shared libs.
sed -i -e 's/LD_LIBRARY_PATH/MCR_LIBRARY_PATH/g' /MY/PACKAGE/BUILD/PATH/__init__.py
Then obviously export MCR_LIBRARY_PATH before using python.

TCLBLEND FAILURE - Centos 6.4

I have been trying to use a home grown test tool and after doing an update to Centos 6.4, I am no longer able to run the tcl based tool. I am getting the following error and I have no internet access on this server. Kindly advise how do I solve this problem?
Thanks
"XpUtils::iload -d /usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1 tclblend" failed:
couldn't load file "/usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1/libtclblend.so": libjava.so: cannot open shared object file: No such file or directory
while executing
"error "\"XpUtils::iload -d $dir tclblend\" failed:\n $errMsg""
(procedure "loadtclblend" line 168)
invoked from within
"loadtclblend /usr/local/testtool/repo/package/linux-glibc2.3-x86_64/lib/tcljava1.4.1"
("package ifneeded java 1.4.1" script)
invoked from within
"package require java"
("eval" body line 1)
invoked from within
"eval package require $pkg"
("foreach" body line 2)
invoked from within
"foreach pkg $pkgList {
set ::${pkg}Version [eval package require $pkg]
}"
(file "/usr/local/testtool/testtool" line 165)

If you read the error message trace, you'll see that it says that this is all caused by:
libjava.so: cannot open shared object file: No such file or directory
The first steps would then be to ensure that you've got a version of Java actually installed, to check that it includes the file libjava.so, and that the file has been indexed by the system shared library catalog.
It might also be worth checking that all its dependencies are also present and that you've got the architecture for the Tcl library and the Java library matched (e.g., both 32-bit) as those can cause odd failures when they go wrong.

Magic value error when I run my applet

I create an Applet and I generate the jar file with the following code
JAR FILE
"c:\arquivos de programas\java\jdk1.7.0_05\bin\jar" cvf C:\Users\lucas\Desktop\AbrirAplicativo3000.jar C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\WebcamApplet.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\QRCodeProcessor.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\QRCodeListener.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\OpenCVWebCam.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\CVImageProcessor.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\AbstractProcessor.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\gui\ImagePanel.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\gui\LabelPanel.class C:\Users\lucas\workspace\WebcamApplet\bin\com\colorfulwolf\webcamapplet\gui\LoadingScreen.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\StringsResourceTranslator.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\client\j2se\BufferedImageLuminanceSource.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\client\j2se\CommandLineRunner.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\client\j2se\GUIRunner.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\client\j2se\ImageConverter.class C:\Users\lucas\workspace\WebcamApplet\bin\com\google\zxing\client\j2se\MatrixToImageWriter.class
and I singed the JAR file normally.
I put the JAR file in a visible HTTP (http://www.netimoveis.com/AbrirAplicativo3000.jar)
In my ASPX page, I'm calling the APPLET following this code
<applet code="com.colorfulwolf.webcamapplet.WebcamApplet"
archive="http://www.netimoveis.com/AbrirAplicativo3000.jar, http://www.netimoveis.com/AbrirAplicativoAssinado3000.jar"
height="550" width="550">
</applet>
But when I try to run, I got the error
Incompatible magic value 218774561 error in applet
Someone can help me ?

Your AbrirAplicativo3000.jar is not correctly packaged. If you look inside, it has this structure:
META-INF/
C:/
Users/
lucas/
workspace/
WebcamApplet/
bin/
com/ --> this is where the jar should start from.
...
Try using the -C option on the jar command like this:
"c:\arquivos de programas\java\jdk1.7.0_05\bin\jar" cvf C:\Users\lucas\Desktop\AbrirAplicativo3000.jar -C C:\Users\lucas\workspace\WebcamApplet\bin\ .
Also it's not the first time that this magic number comes up on SO, although it seems more related with a bad URL. However I did download the jar with your supplied URL so just try re-packaging it.

The magic value error means that the class file doesn't start with the integer 0xCAFEBABE as it should. You probably had a transfer or compression problem.
If you can open the file in an hex editor, you may look for those bytes.

Protocol Buffers Invalid embedded descriptor problem

I'm having some problems at runtime with some of my generated protocol buffer classes.
My project layout is as follows:
module/
protobuf-api/
proto/
com/foo/api/Service.proto
com/foo/shared/Shared.proto
org/bar/api/Message1.proto
org/bar/api/Message2.proto
The Service.proto file depends on Shared.proto and some of the Message*.proto files. From the protobuf-api directory, I run the following command to compile:
find . -name *.proto -exec protoc --java_out=java -I=proto {} \;
When I attempt to run my Service, I get the following exception:
java.lang.ExceptionInInitializerError
at com.linkedin.history.api.protobuf.HistoryServiceProtos$HistoryServiceQuery.(HistoryServiceProtos.java:544)
at com.linkedin.history.api.serializer.HistoryServiceSerializer.serialize(HistoryServiceSerializer.java:47)
at test.history.serializer.TestSerializer.testHistoryServiceQuery(TestSerializer.java:38)
at test.fwk.util.core.BaseTestSuiteCore.run(BaseTestSuiteCore.java:304)
at test.fwk.util.core.BaseTestSuiteConf.run(BaseTestSuiteConf.java:186)
at test.fwk.lispring.BaseTestSuite.run(BaseTestSuite.java:232)
at test.fwk.lispring.BaseTestSuite.callAppropriateRun(BaseTestSuite.java:265)
at test.fwk.util.core.BaseTestSuiteCore.run(BaseTestSuiteCore.java:199)
Caused by: java.lang.IllegalArgumentException: Invalid embedded descriptor for "com/linkedin/history/api/protobuf/HistoryService.proto".
at com.google.protobuf.Descriptors$FileDescriptor.internalBuildGeneratedFileFrom(Descriptors.java:268)
at com.linkedin.history.api.protobuf.HistoryServiceProtos.(HistoryServiceProtos.java:1794)
Caused by: com.google.protobuf.Descriptors$DescriptorValidationException: com/linkedin/history/api/protobuf/HistoryService.proto: Dependencies passed to FileDescriptor.buildFrom() don't match those listed in the FileDescriptorProto.
at com.google.protobuf.Descriptors$FileDescriptor.buildFrom(Descriptors.java:221)
at com.google.protobuf.Descriptors$FileDescriptor.internalBuildGeneratedFileFrom(Descriptors.java:266)
I've read the post here but I think I'm doing everything correctly. Any suggestions on why I'm having the initializer errors? I'm compiling everything with the same -I flag.

I suspect that the problem is that when you're finding the proto file, you've given it the full path, e.g. proto/com/foo/api/Service.proto but when it refers to it via the include directory, it's using com/foo/api/Service.proto
Simple fix - run this from the proto directory:
find . -name *.proto -exec protoc --java_out=../java -I=. {} \;
I must admit I can't remember a lot of the details of protoc (which I really should) but I suspect that will work.
Another alternative which may work:
protoc --java_out=java `find . -name '*.proto'`
i.e. pass all the proto files into a single call to protoc.

I had the same error type in C# and here was my problem: I called the protoc in a pre-build step in my project. There I used Visual Studio built-in macros like $(SolutionDir) and $(ProjectDir) to retrieve necessary paths. Since I referenced *.proto files from other projects, I used two --proto_path options: one for the root path (to resolve import paths) and one for the file itself. My solution file was inside a subdirectory of the root directory, so I used the relative path .. to get to the root. Proto files are always in subdirectory gen of the particular project. All in all, the command was like this:
protoc.exe --proto_path=$(SolutionDir).. --proto_path=$(ProjectDir)gen $(ProjectDir)gen\DemoFile.proto
It compiled fine, but I got the System.TypeInitializationException at runtime on calling CreateBuilder() method. The problem was that both paths $(SolutionDir).. and $(ProjectDir) (though effectively pointing to the same directory) had different textual representation due to the relative path component ... I solved the problem by consistently using the same path like this:
protoc.exe --proto_path=$(SolutionDir).. $(SolutionDir)..\My\Demo\Project\Directory\gen\DemoFile.proto
It cost me almost 3 days to narrow down and recognize the problem, so I share my solution here in hope that it will save some time for someone.