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Java Jython RDKit, some progress, still confused

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  Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-16 15:54 +0000
    Re: Java Jython RDKit, some progress, still confused Martin Gregorie <martin@mydomain.invalid> - 2020-06-16 19:54 +0000
      Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-07 12:40 +0000
        Re: Java Jython RDKit, some progress, still confused Martin Gregorie <martin@mydomain.invalid> - 2020-07-07 13:09 +0000
          Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-07 18:06 +0000
            Re: Java Jython RDKit, some progress, still confused Martin Gregorie <martin@mydomain.invalid> - 2020-07-07 19:23 +0000
              Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-07 20:11 +0000
                Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-08 11:32 +0000
                  Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-08 13:40 +0000
                    Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-08 15:30 +0000
                      Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-08 17:04 +0000
                        Re: Java Jython RDKit, some progress, still confused "C.D. Altenburg, Ph.D," <cdalten@gmail.com> - 2020-07-08 11:13 -0700
                          Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-08 18:33 +0000
                        Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-07-08 22:19 +0200
                      Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-07-08 22:23 +0200
                        Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-11 19:12 +0000
                          Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-12 17:24 +0000
                            Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-07-21 01:46 +0200
    Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-16 22:32 +0200
      Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-16 20:40 +0000
        Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-17 15:58 +0000
          Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-17 20:43 +0000
          Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-18 16:15 +0200
            Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-18 18:40 +0000
    Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-12 17:42 +0000
    Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-12 18:12 +0000
      Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-13 13:31 +0000
        Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-13 18:34 +0000
          Re: Java Jython RDKit, some progress, still confused Eric Sosman <esosman@comcast-dot-net.invalid> - 2020-07-13 16:13 -0400
            Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-16 16:29 +0000
            Re: Java Jython RDKit, some progress, still confused vjp2.at@at.BioStrategist.dot.dot.com - 2020-07-16 16:32 +0000
              Re: Java Jython RDKit, some progress, still confused "C.D. Altenburg, Ph.D," <cdalten@gmail.com> - 2020-07-17 08:42 -0700
              Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-07-21 01:53 +0200
                Re: Java Jython RDKit, some progress, still confused Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-07-21 01:55 +0200
    Re: Java Jython RDKit, some progress, still confused rahul kumar <lingmaaki@gmail.com> - 2020-09-15 22:41 -0700

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#39513

Same error  "could not find the main class"

Got rid of the -cp and -jar and again, same error

Found something online that rnning a program as
java x.class intread of java x causes this problem

But I'm still stumped why they complied something used in classpath as .jar
instead of .class

YOu can find out about my setup by google <jython rdkit>

https://www.baeldung.com/java-could-not-find-load-main-class


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39515

On another machine/OS I played with kawa/jemacs - exact same error

it's like
java -jar kawa.jar emacs.elisp

I looked repeatedly, there is no separate emacs file, it runs form within
kawa




				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39520

On 2020-06-17 17:58, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> Same error  "could not find the main class"
> 
> Got rid of the -cp and -jar and again, same error
> 
> Found something online that rnning a program as
> java x.class intread of java x causes this problem
> 
> But I'm still stumped why they complied something used in classpath as .jar
> instead of .class
> 
> YOu can find out about my setup by google <jython rdkit>
> 
> https://www.baeldung.com/java-could-not-find-load-main-class
> 

JARs normally declare their Main (entry point) class in
META-INF/MANIFEST.MF. Maybe the version you have doesn't. Again, I would
encourage you to download an up-to-date version of jython-standalone.

Also, in order to eliminate mistakes stemming from the complex setup,
you should start by seeing whether you're able to run a simple script,
as I illustrated.

-- 
DF.

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#39521

Ok, but jython works fine.
I ran it days ago.
In fact, I copied it to my java directory for other use

THe other thing I want to track down the original batch file
which had stuff like Xm256x which I removed until Java ran

I may not be back at it until Wednesday, tho
Other issues more pressing

				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39560

I found this, how do you explain the quotes and semicolons??

I would have a problem with the quotes because I already have "%..%"

https://stackoverflow.com/questions/11727440/having-trouble-setting-java-library-path-for-jython

"C:\Program Files\Java\jdk1.6.0_31\bin\java.exe" -Xint "-Dpython.path=c:\scm\main\core\isidurandal\durandal\scripts\lib" "-Dpython.home=c:\bin\jython2.5.2" "-Djava.library.path=c:\scm\main\core\isidurandal\durandal\build" -classpath "c:\bin\jython2.5.2\jython.jar;c:\scm\main\core\isidurandal\durandal\build\durandal.jar;c:\scm\main\core\isidurandal\japanese\build\durandalJapanese.jar;c:\scm\main\core\isidurandal\biometrics\build\MtiBiometrics.jar" org.python.util.jython  tools\alignSequences.py




				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39561

I  used single quotes. no spaces before or after the semicoln.
I get the java help message list of options.
I can't cut & past the top half


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39562

"%JAVA_COMMAND%" -Xmx256m -classpath
'"%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper\org.RDKit.jar;"%JAVA_HOME%"\bin\jython-standalone-2.5.4-rc1.jar.jar'
-Djava.library.path="%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper

The system cannot find the path specified. '-Djava.library.path' is not
recognized as.. no diff if i put it in '' or not.. ditto the -X

Previously:

java.lang.NoClassDefFoundError java.lang.ClassNotFoundException:
org.RDKit.jar Could not find the main class


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39563

Some mention 32 v 64 bit as the source of this problem.
-version gives 1.6.0_25.B06 no mention of 64bit
Am I safe that it is 32 bit java?


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39564

On 7/13/2020 2:34 PM, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> Some mention 32 v 64 bit as the source of this problem.
> -version gives 1.6.0_25.B06 no mention of 64bit
> Am I safe that it is 32 bit java?

     Java 6 came in both 32- and 64-bit versions on at least some
platforms.  I'm surprised the -version message doesn't say anything
about the matter; you might want to double-check.

     By the way, note the past tense of "came" above.  Java 6 was
released almost fourteen years ago, went off free support seven
years ago, and Oracle stopped selling extended maintenance contracts
for it two and a half years ago.  Unless there's some pressing reason
to run an outdated, unsupported, and insecure ("no patches for seven
years") version, consider an upgrade.  Java 6 is roughly contemporaneous
with Windows Vista ...

-- 
esosman@comcast-dot-net.invalid
Trump "aced his cognition test" but can't recall the questions.
One hundred ninety-one days to go.

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#39566

*+-    Java 6 came in both 32- and 64-bit versions on at least some

Thanks much. Dunno if i can trust them but various searches say if it doesn't
say 64-bit, the it is 32-bit. Which is what I want it to be.
But that would have explained some of my errors.



				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39567

I'm really tired of this, so I can see why others might be too.
Profue apologise and many thanks for your patience.

But I broke it down to defined files.dirs, dir dir lists of them to be sure
they weren't typos. THe rror messages are not all for this version, I just
accumulated them and I fully expect them to reappear ('.`)

@echo off
SET RD_HOME=.
SET JAVA_HOME=..\CommonFiles\JAVA
SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
SET rdk=%RD_HOME%\rdkit-master\Code\JavaWrappers\gmwrapper\org.RDKit.jar
set jyt="%JAVA_HOME%"\bin\jython-standalone-2.5.4-rc1.jar.jar
set jlp="%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper
 
rem -verbose:class 
 
"%JAVA_COMMAND%"    -Xmx256m  -classpath "%rdk%;%jyt%" -Djava.library.path=%jlp%  | more

pause 


rem Loaded java.lang.Shutdown  lib\rt.jar

rem from java import lang works only if preceded by from java.lang import *

rem ImportError: No module named RKDit

rem java.lang.NoClassDefFoundError java.lang.ClassNotFoundException: org.RDKit.jar Could not find the main class:

rem The system cannot find the path specified. '-Djava.library.path' is not recognized as

rem help() ImportError: No module named pydoc
 
rem | "%RD_HOME%"\rdkit.py 
:END


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39569

Go away you fucking moron.

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#39576

On 2020-07-16 18:32, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> I'm really tired of this, so I can see why others might be too.
> Profue apologise and many thanks for your patience.
> 
> But I broke it down to defined files.dirs, dir dir lists of them to be sure
> they weren't typos. THe rror messages are not all for this version, I just
> accumulated them and I fully expect them to reappear ('.`)
> 
> @echo off
> SET RD_HOME=.
> SET JAVA_HOME=..\CommonFiles\JAVA
> SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
> SET rdk=%RD_HOME%\rdkit-master\Code\JavaWrappers\gmwrapper\org.RDKit.jar
> set jyt="%JAVA_HOME%"\bin\jython-standalone-2.5.4-rc1.jar.jar
> set jlp="%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper
>  
> rem -verbose:class 
>  
> "%JAVA_COMMAND%"    -Xmx256m  -classpath "%rdk%;%jyt%" -Djava.library.path=%jlp%  | more
> 
> pause 
> 
> 
> rem Loaded java.lang.Shutdown  lib\rt.jar
> 
> rem from java import lang works only if preceded by from java.lang import *
> 
> rem ImportError: No module named RKDit
> 
> rem java.lang.NoClassDefFoundError java.lang.ClassNotFoundException: org.RDKit.jar Could not find the main class:
> 
> rem The system cannot find the path specified. '-Djava.library.path' is not recognized as
> 
> rem help() ImportError: No module named pydoc
>  
> rem | "%RD_HOME%"\rdkit.py 
> :END
> 

The syntax for launching Java (well, one of them, but the one you want) is:
java.exe [OPTIONS] -classpath [CLASSPATH] -jar [JYTHON-JAR] [JYTHON
ARGUMENTS]

Replace "from java import lang" with "from java.lang import *", as the
warning tells you, then run:

"%JAVA_COMMAND%" -Xmx256m -classpath "%rdk%" -jar %jyt
-Djava.library.path=%jlp% [PATH TO YOUR PYTHON SCRIPT]

I'm pretty sure it's not rocket science. You just gotta be careful with
the details.

-- 
DF.

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#39577

On 2020-07-21 01:53, Daniele Futtorovic wrote:
> "%JAVA_COMMAND%" -Xmx256m -classpath "%rdk%" -jar %jyt
> -Djava.library.path=%jlp% [PATH TO YOUR PYTHON SCRIPT]

That should be "-jar %jyt%" (missed the closing percent).

-- 
DF.

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#39612

While executing, when JVM does not find a .class file with the specified name then a run time error occurs saying “Could not found or load main class”. The reason why this happens is mostly due to:

Wrong Class Name
Invalid Classpath

Main class could not be found when there is typo or wrong syntax in the fully qualified class name or it does not exist in the provided classpath. You must ensure that you add the location of your .class file to your classpath. So, if its in the current folder, add . to your classpath. Note that the Windows classpath separator is a semi-colon( ;) .  If you want to execute the main() method in MainClass, you must use the full class name, including package name, in the java command.

http://net-informations.com/java/cjava/default.htm

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