MolSearchExample.java does not compile

Hello:

I am trying to run the example MolSearchExample.java located in ~/Chemaxon/JChem5.2/examples/java/search and I have added to my CLASSPATH the following:

$ printenv CLASSPATH

/usr/share/java/mysql.jar:/home/roberto/ChemAxon/JChem5.2/lib/jchem.jar:/home/roberto/ChemAxon/JChem5.2/marvin/sjars/util.jar

though as some point CLASSPATH had most of the jar files on ~/Chemaxon/lib. When I try to compile, I get the next error:

$ javac MolSearchExample.java 

MolSearchExample.java:53: cannot find symbol

symbol  : variable Util

location: class search.MolSearchExample

new FileInputStream(Util.addPath("t.mrv")));

                   ^

MolSearchExample.java:79: cannot find symbol

symbol  : variable Util

location: class search.MolSearchExample

System.out.println(Util.dumpIntArray(hit));

                  ^

MolSearchExample.java:89: cannot find symbol

symbol  : variable Util

location: class search.MolSearchExample

System.out.println(Util.dumpInt2DArray(hitAll));

                  ^

3 errors

Maybe I should add that also DuplicateSearch.java presents itself with similar issues, though this time it also cannot find the MoleculeImport module:

$ javac DuplicateSearch.java 

DuplicateSearch.java:41: cannot find symbol

symbol  : variable Util

location: class search.DuplicateSearch

   Util.standardInputFile());

   ^

DuplicateSearch.java:40: cannot find symbol

symbol  : variable MoleculeImport

location: class search.DuplicateSearch

   Molecule[] mols = MoleculeImport.moleculeArrayImport(

                     ^

Note: DuplicateSearch.java uses unchecked or unsafe operations.

Note: Recompile with -Xlint:unchecked for details.

2 errors

Hi,

The files in the example directory use other java files in the same directory, e.g. Util.java. In order to enable their usage the examples/java directory should be included.

In your case please include: ~/Chemaxon/JChem5.2/examples/java in the CLASSPATH as well.

Then you should be able to compile and the run the example file (java search.MolSearchExample
).

The same is true for the other example file.

Bye,

Robert

Robert:

Thank you for your reply. I successfully compiled Util.java. In order to make DuplicateSearch.java work, I also need the MoleculeImport class to work. So I try to compile this and get the following error:

$ javac MoleculeImport.java 


MoleculeImport.java:61: cannot find symbol


symbol  : variable Util


location: class search.MoleculeImport


		    localPath ? Util.addPath(path) : path );


		                ^

This is the CLASSPATH I'm using (please disregard the 5.2 of my previous e-mail):

$ echo $CLASSPATH


/usr/share/java/mysql.jar:/home/roberto/ChemAxon/JChem/lib/jchem.jar:/home/roberto/ChemAxon/JChem/marvin/sjars/util.jar:/home/roberto/ChemAxon/JChem/examples/java/search/Util.class:/home/roberto/Chemaxon/JChem/examples/java/search:/home/roberto/Chemaxon/JChem/examples/java

Hi Roberto,

Please paste the output of:

ls /home/roberto/Chemaxon/JChem/examples/java

then execute:

CLASSPATH=/home/roberto/ChemAxon/JChem/lib/jchem.jar:/home/roberto/ChemAxon/JChem/examples/java

and

javac /home/roberto/ChemAxon/JChem/examples/java/search/MolSearchExample.java

what are the outputs?

Bye,

Robert

Robert,

After postponing this problem for long enough, I finally got the example to compile, following your instructions (in the previous mesages:

$ javac -verbose ~/ChemAxon/JChem/examples/java/search/MolSearchExample.java

However, I cannot get this program to run:

$ java MolSearchExample
Exception in thread "main" java.lang.NoClassDefFoundError: MolSearchExample
Caused by: java.lang.ClassNotFoundException: MolSearchExample
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

Any thoughts?

Thanks,

Roberto

CLASSPATH problem again: you should make sure the class file you created can be found via the CLASSPATH.

Most Java books give a good overview of the classpath and package hierarchy - this is an important concept to understand when starting to program in Java.