Hi Eric There are two folders in directory C:\Program Files\Java\ (In my opinion, the lib subdirectory speicfied by you is the lib of Java, and no lib folder is found in TPP installed directories.), jre1.5.0_03 and jre6.
Under the subdirectory of lib in jre1.5.0_03, the .jar files are: deploy.jar, jce.jar, plugin.jar, javaws.jar, jsse.jar, rt.jar, with subdirectories: images, javaws, applet, classlist, cmm, ext, management, security, fonts, tzmappings, i386, zi, im. Under the subdirectory of lib in jre 6, .jar files are: charsets.jar, management-agent.jar, deploy.jar, plugin.jar, javaws.jar, resources.jar, jce.jar, rt.jar, jsse.jar; and subfolders are: applet, audio, management, classlist, cmm, deploy, ext, security, servicetag, fonts, i386, tzmappings, im, zi, images. None of the .jar files mentioned are found under the subdirectories of lib and the directories under lib. Thanks very much. 2012/3/2 Eric Deutsch <[email protected]> > Hi Elkan, can you describe your situation a little more? Is there a lib > directory? What is in it? Are **some** of the jars there, just not all? > Or it’s not there at all? > > > > Thanks, > > Eric > > > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Naiheng Dong > *Sent:* Tuesday, February 28, 2012 7:48 PM > *To:* [email protected] > *Subject:* Re: [spctools-discuss] Re: Problem in running QualScore in TPP > v4.5.2 > > > > Hi Eric > > Thanks for your reply. > > All of the .jar files listed by you do not appear in the subdirectory > called lib. > > So how can I repair it? > > Elkan > > 在 2012年2月29日 上午11:26，Eric Deutsch <[email protected]>写道： > > Hi Elkan, I think for QualScore to work, all the supplemental jars like > jfreechart-0.9.15.jar need to be in the subdirectory called lib for things > to work. So when you execute "java -jar qualscore.jar", it is expecting to > find all these files: > > lib/TableLayout.jar lib/jcommon-0.9.0.jar lib/jfreechart-0.9.15.jar > lib/jrap.jar lib/jscicore.jar lib/log4j-1.2.8.jar lib/msutils.jar lib/tar. > jar lib/trove.jar lib/xercesImpl.jar > > Are they there? > > Eric > > > > > > -----Original Message----- > > From: [email protected] [mailto:spctools- > > [email protected]] On Behalf Of Jorey Dong > > Sent: Tuesday, February 28, 2012 5:18 PM > > To: spctools-discuss > > Subject: [spctools-discuss] Re: Problem in running QualScore in TPP > > v4.5.2 > > > > Hi Damian > > > > Thanks for your kind help. > > > > When I type the command "java -jar qualscore.jar" in the Windows > > command line after moving to directory C:\Inetpub\tpp-bin, error still > > occurs, as listed below: > > " > > Exception in thread "main" java.lang.NoClassDefFoundError: org/jfree/ > > data/SeriesDataset > > Caused by: java.lang.ClassNotFoundException: > > org.jfree.data.SeriesDataset > > at java.net.URLClassLoader$1.run(Unknown Source) > > at java.security.AccessController.doPrivileged(Native Method) > > at java.net.URLClassLoader.findClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > Could not find the main class: > > org.systemsbiology.qualscore.commandline.Main. Program will exit. > > " > > > > Does it mean that the Java Environment I installed is not appropriate? > > > > Best Regards. > > > > Elkan > > > > On 2月29日, 上午12时33分, GATTACA <[email protected]> wrote: > > > Try executing qualscore from the Windows command line: > > > cd C:\Inetpub\tpp-bin > > > java -jar qualscore.jar > > > > > > Executing the above commands should give you a usage statement for > > > Qualscore if everything is okay. > > > After that, it's just a question of passing it the write parameters. > > > > > > Damian > > > > > > On Feb 28, 9:00 am, Jorey Dong <[email protected]> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > Hi All, > > > > > > > When I run QualScore embedded in TPP to assess the quality of > > tandem > > > > mass spectra, the error occurs: > > > > " > > > > run_in c:/Inetpub/wwwroot/ISB/data; java -jar c:\Inetpub\tpp-bin > > > > \qualscore.jar -c 1.0 -p 0.1 -a 20060502data06.xml > > > > > > > java.lang.NoClassDefFoundError: org/jfree/data/SeriesDataset > > > > Caused by: java.lang.ClassNotFoundException: > > > > org.jfree.data.SeriesDataset > > > > at java.net.URLClassLoader$1.run(Unknown Source) > > > > at java.security.AccessController.doPrivileged(Native > > Method) > > > > at java.net.URLClassLoader.findClass(Unknown Source) > > > > at java.lang.ClassLoader.loadClass(Unknown Source) > > > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown > > Source) > > > > at java.lang.ClassLoader.loadClass(Unknown Source) > > > > Could not find the main class: > > > > org.systemsbiology.qualscore.commandline.Main. Program will exit. > > > > Exception in thread "main" > > > > command "java -jar c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 - > > a > > > > 20060502data06.xml" failed: Operation not permitted > > > > > > > Command FAILED > > > > " > > > > > > > Same error occurred when I run the data PeptideProphet output file > > > > interact-20060502data06.xml. > > > > > > > So any one can help me solve this problem? > > > > > > > Best Regards. > > > > > > > Elkan > > > > -- > > You received this message because you are subscribed to the Google > > Groups "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to spctools- > > [email protected]. > > For more options, visit this group at > > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > > > > -- > Naiping Dong (Elkan) > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- Naiping Dong (Elkan) -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
