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Matlab Compiler MCC errors on imports for Java classes from dynamic Java classpath

How can I get mcc to recognize imports from user-provided Java libraries, or to simply ignore unresolvable imports?
I have a Matlab codebase that I'm building with the Matlab Compiler, but the build is breaking because mcc is erroring out when it encounters import statements for Java classes that were in JARs on Matlab's dynamic classpath. I am including all the JAR files on the classpath with the mcc -a option. The code works in the IDE, and I think it will work in the deployed app, if it will only allow me to build. (Works under R2009b, which ignores these imports in non-MCOS classes.)
Here's a simple repro. This file is in the same dir as guava-11.0.1.jar from Google Guava.
%file hello_world_with_import.m
function hello_world_with_import
import com.google.common.base.Stopwatch;
disp('Hello, world!');
end
Running it in Matlab works fine. But building it fails. (The javaaddpath here is not strictly necessary in the example, because bad imports by themselves are not an error in plain Matlab. Just showing how it works in practice, and how I wish mcc picked up on it.)
>> javaaddpath('guava-11.0.1.jar');
>> hello_world_with_import()
Hello, world!
>> mcc -m -a guava-11.0.1.jar hello_world_with_import
Error: File: C:\Temp\import_test\hello_world_with_import.m Line: 3 Column: 8
Arguments to IMPORT must either end with ".*"
or else specify a fully qualified class name: "com.google.common.base.Stopwatch" fails this test.
Unable to determine function name or input/output argument count for function
in MATLAB file "hello_world_with_import".
Please use MLINT to determine if this file contains errors.
Error using mcc
Error executing mcc, return status = 1 (0x1).
This is in Matlab R2011b on Windows.
Some background on my environment. My app has about 40 JARs on the dynamic classpath which are a mix of third party libraries and our own Java code. It's deployed to 50+ users on a mix of single-user and multi-user Windows machines. And there are other groups that may be deploying other MCR apps to the same users and machines. On any machine, different MCR apps may be run concurrently by the same or different users. We do weekly releases, and (mostly due to changes in our own Java code) at least one JAR file changes about every other release. I need a mechanism that will work in this environment.
Any suggestions? Anybody know a good way to get mcc to add stuff to its java classpath in the compilation step, or just ignore bogus imports? My fallback plan is to go through the codebase and remove all the imports for Java classes, which is kind of a pain.
UPDATE 12/2/2012: I heard from MathWorks that this is fixed in Matlab R2012b. (But I'm no longer using Matlab so can't personally verify it.)
UPDATE 12/09/2014: I'm using Matlab again (R2014b), and the Matlab Compiler now includes JARs that are on the dynamic classpath in the compiled program's dynamic classpath. It doesn't seem to automatically include the JAR files in the archive, though; you must manually include them using an mcc command line switch, or adding them as "additional included files" in the Matlab Compiler app.

The code executing in the MATLAB IDE works because the guava jar file has been added to the "dynamic" classpath via the javaaddpath method. However, when you use MCC to invoke the MATLAB Compiler, it does not rely on the dynamic java classpath, but the "static" java classpath which is defined in:
$MATLABROOT/toolbox/local/classpath.txt
If you add an entry for your JAR file here, then MCC will be able to resolve the IMPORT line in your M-File.
So to test this, I downloaded the guava jar file and tried the steps above. Works like a charm.
Also, If you read the "Troubleshooting" section for the MATLAB Compiler, this exact situation is documented:
http://www.mathworks.com/help/toolbox/compiler/brtm1xm-8.html
Quoting from the link: "The import statement is referencing a Java class () that MATLAB Compiler (if the error occurs at compile time) or the MCR (if the error occurs at run time) cannot find.
To work around this, ensure that the JAR file that contains the Java class is stored in a folder that is on the Java class path. (See matlabroot/toolbox/local/classpath.txt for the class path.) If the error occurs at run time, the classpath is stored in matlabroot/toolbox/local/classpath.txt when running on the development machine."

You just have to put import statements in a separate .m file.
so from:
javaaddpath 'c:\some.jar';
import com.something.Element;
...interesting stuff...
There will be a do_imports.m:
import com.something.Element;
And in original .m:
javaaddpath 'c:\some.jar';
do_imports
...interesting stuff...
And then it will compile and work. No need to mess around with system-wide classpaths.

Here is an extract from the link
http://blogs.mathworks.com/desktop/2009/07/06/calling-java-from-matlab/
MATLAB maintains a path for Java classes separate from the search path. That means even if you have a .class or .jar file on the MATLAB path, unless you use javaaddpath you will not be able to use it. To see what is currently on the path use javaclasspath. Running this command you will show you a long list of files that ship with matlab called the Static Class Path and then you'll see the Dynamic Class Path. The dynamic class path is where classes added to the path with javaaddpath will be placed. They can be removed with javarmpath and have to actively reloaded each session of matlab.

Compiling and running a Java program on a Mac

This is an extremely basic question, but I haven't been able to find the answer anywhere. I'm completely new to Java.
There's a Java program on github that I'm trying to get running on my Mac. The associated documentation does not give any information on compiling or running the code. I would prefer not disclosing in any more detail the specific program I'm trying to run.
The program contains multiple .java files and a classmexer.jar file for tracking memory usage. There is also a subfolder, cern, that contains additional subfolders that ultimately contain .class files. There is no makefile.
I've downloaded all of the source code as a tar.gz file and unwrapped it into ~/codeDirectory/. When I try to compile from this directory with
$ javac *.java
or
$ javac A.java
(where A.java is the first class that program calls), I get dozens of compile errors. This code clearly compiles successfully elsewhere, so I'm unsure what to make of this.
The first error that appears is
A.java:5: cannot access cern.colt.function.DoubleFunction
class file for cern.colt.function.DoubleFunction not found
cern.jet.random.AbstractDistribution.makeDefaultGenerator();
^
./B.java:4: package com.javamex.classmexer does not exist
import com.javamex.classmexer.*;
^
./B.java:180: cannot find symbol
symbol : variable MemoryUtil
location: class B
long noBytes = MemoryUtil.deepMemoryUsageOf(hp);
^
My suspicion is that there's an improperly or incorrectly specific path somewhere, but I haven't been able to find it.
Thanks in advance for any help troubleshooting.

If you downloaded a Java program from github, it's nearly certain that it comes with a build.xml for use with Apache Ant, or a pom.xml for use with Apache Maven, or some other file for use with some other build tool. Typically, a code base on github will have documentation telling you what tool to use and how to use it.

The program I was attempting to run was incomplete and did not include the source code for two dependencies (including colt, which the compiler flagged above). Thanks to Anony-Mousse for suggesting this option. Installing all the necessary source code solved the problem; the developer has also updated the files.

Compiling Java package throws errors for external Jars

Pretty basic problem here. So I have a Java package that I have created that has three classes (one has the main method). I am trying to use a few Apache Jars, and have added these to my build path in Eclipse. However Eclipse wont let me build and run it properly, so I am trying the command line. I have added the env var CLASSPATH and pointed it to my lib directory which hold the Apache Jars. However, when I try to use javac I get a bunch of errors:
package org.apache.xmlrpc does not exist
import org.apache.xmlrpc.client.XmlRpcClient;
I was reading the man page for javac and it said that:
If neither CLASSPATH, -cp nor -classpath is specified, the user class path consists of the current directory.
So I tried copying the Jars to the same location as my three source files, but no change.
Can someone please tell me what I'm doing wrong?
Thanks.

Classpath variable (or command line option of javac) must contain all jars explicitly. It cannot go through jar files stored in specified directory.

You can compile this by specifying the option -cp on the command line:
javac -cp foo.jar:bar.jar foo/bar/Baz.java
You then run it with the same option:
java -cp foo.jar:bar.jar foo.bar.Baz

It sounds like you've just set the classpath to the directory containing the jar files. You need to set it to the individual jar files, or use java.ext.dirs to set an "extension" directory containing jar files. I'd recommend using the specific jar files. Something like:
// Assuming Windows...
CLASSPATH = c:\libs\foo.jar;c:\libs\bar.jar
I'd also personally recommend specifying the classpath on the command line instead of using an environment variable - the latter will work, but it ends up being a bit more fiddly if you want to compile different projects against different libraries.
However, I'd actually recommend getting Eclipse working first, rather than retreating to the command line. It should be fine - if you could give us more information about what's failing in Eclipse, we may be able to help you with that instead.

The jar files in the current directory are not automatically included; that only refers to .class files in normal package/directory hierarchy. Jar files must be added either explicitly, or via a wildcard like javac -cp ./* (Assuming JDK6+)
(Some OSes may require an escape of the * to avoid globbing; OSX does not.)

I agree with previous answers, but I would also recommend to use proper java build tool - like ant (perceived easier to use, but not necessary) or maven ( perceived more difficult to use, but really worth learning )

compiling multiple java classes in linux

i used netbeans to code the classes and they are all included in a package but when i try to compile the application class in linux it spits out errors on class definitions for the classes i am working with. points at the class names for the objects and says "cannot find symbol" i need help!!!

use javac -sourcepath < your source code path >
Better check -help option as it mostly solve your problems

cd to the directory containing your package then run:
javac -classpath . your_package_name/*

I'm not a Java guru, but I have a small java project that I developed years ago and have recently ported to compile with javac on Linux.
I got this to work in two different ways:
Created a single Java source file that held all of my classes
Put each of my classes in a separate file but all in the same directory
In each case, I can compile and run with the following:
javac *.java && java name_of_main_class
Notice that I did not specify a "-classpath" option when I compiled. I guess this works because I have not used a directory substructure or created a package. If you are dealing with those issues, this page appears to have some examples that may help you: Help with packages in java - import does not work
A key thing to understand about Java packages: They correspond to subdirectories where the classes are defined (or to JAR files which just bundle and compress those subdirectories into a single file). Therefore, anytime you specify the package keyword in your source, you need to make sure that the source files (and the class files) are distributed to subdirectories correspondingly. The -classpath option to javac may provide a workaround when subdirectory structures do not exactly match what is specified by the package keyword.

If you built the project using NetBeans, you can use Ant to build the project on command line. NetBeans generate Ant Build script.
just cd into the directory where the project is located then type 'ant'
it should build the project for you automagically

Can I add classes to sun's rt.jar file?

I downloaded the Javax.mail package. I have jdk1.6.0_11.
Problem is...I cannot get javac or java to find those classes!
I can get apps to compile using JCreator LE ( by adding the mail jar
to its search list ) but, when I try to run the app in a command window,
it fails.
Can I add these new classes to the rt.jar without
hurting my jdk installation?
I know java has it wired up to look there for classes.
(And, the mail classes are inside a javax package - seems like
they could reasonably be added to the javax folder in rt.jar..
Thanks!
Phil D'

No you can't, nor should you.
Instead, figure out the problem with your classloader (probably paths?). You'll need that for the next library you need to access.
Messing with rt.jar means you can't run on any other JVM.

You should either specify the jar file in your classpath: preferably on the command line with the -cp option, but possibly with the CLASSPATH environment variable.
Alternatively, you can specify its directory in the java.ext.dirs system property. For more details, see the documentation for the extensions mechanism.
You shouldn't be messing around with rt.jar. That's very definitely not the way to make extra jar files available - it's akin to trying to add Microsoft Word to the Windows kernel ;)

Adding things to rt.jar seems like a bad idea, even though its possible and easy to accomplish.
Try compile your application from the command line like this:
javac -cp <path_to_3rd_libs>/jarfile.jar . MainClass.java
If the compiler still complains about the javax.mail package try to unpack/examine the jar file to see that javax.mail package (and its expected content) is there.
(On windows its easy to examine a jar file using 7zip.)

Most definitely no.
If you post the command you are running from the command line we will be able to point you on the right direction, but most likely you are just missing a classpath parameter.
java -classpath /path/to/mail.jar MyClass

You need to understand the CLASSPATH concept which allows you to add individual classes and jar files containing classes to the "universe" of defined classes available for the code you want to compile and/or run. It is similar in idea to the PATH variable in the Windows world.
For the Windows command line this is the documentation:
http://java.sun.com/javase/6/docs/technotes/tools/windows/classpath.html
The Java Tutorial surprised me by not being well-written for this particular concept:
http://java.sun.com/docs/books/tutorial/essential/environment/paths.html
You most likely need something along the lines:
C:> set CLASSPATH=c:\javamail\first.jar;c:\javamail\second.jar
after which both java and javac should know about these classes