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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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Can't initiate the application #6

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by rmcjband...@gmail.com on 9 Jul 2015 at 6:06

GoogleCodeExporter commented 9 years ago 
Thanks for telling us about this. However, I'm not really sure which tool it is 
you are trying to start? Are you referring to the compomics-utilities demo? If 
so, how are you trying to start the tool? As written in the Download section we 
strongly recommend using Maven for this purpose.

Also note that compomics-utilities is mainly a backend library for developers. 
If you're not a developer, I'd recommend rather looking at our more end user 
oriented projects like SearchGUI (http://searchgui.googlecode.com) and 
PeptideShaker (http://peptide-shaker.googlecode.com).

Original comment by harald.b...@gmail.com on 11 Jul 2015 at 8:08

GoogleCodeExporter commented 9 years ago 
I was trying to initiate the SearchGUI-1.30.1.jar file and the 
PeptideShaker-0.41.1.jar files, unfortunately for both applications ended up 
without initiating them properly giving following log file,

Strtup log file

"Memory settings read from the user preferences: 3072
args: 
original java.home: C:\Program Files\Java\jre1.8.0_45\bin\
new java.home: C:\Program Files\Java\jre1.8.0_45\bin\

Command line: 
"C:\Program Files\Java\jre1.8.0_45\bin\java" 
-splash:resources\conf\peptide-shaker-splash.png -Xms128M -Xmx3072M -cp 
"E:\Research Proposal\Proteomis\Bioinformatics for proteomics\Software 
collection\PeptideShaker-0.41.1\PeptideShaker-0.41.1\PeptideShaker-0.41.1.jar" 
eu.isas.peptideshaker.gui.PeptideShakerGUI 
Process exitValue: 1"

My computer operating system is Windows 7, 32 bit and the Java version is 
"1.8.0_45-b15" and probably the 32 bit, because i have installed 32 bit version 
of the Java application in to the OS.

Please be kind enough to be help in this cause.

Thanking you

Original comment by rmcjband...@gmail.com on 11 Jul 2015 at 9:39

GoogleCodeExporter commented 9 years ago 
The problem is that you are trying to use more memory than a 32 bit system is 
able to. 32 bit systems can use maximum 2 GB of memory, while you're trying to 
start the tools with 3 GB.

Could you try deleting the file userpreferences.cup located in a folder called 
".compomics", which you should find in your user home folder (usually in 
"C:\Users\"your user name"\). And then try starting the tools again.

If it still does not work you can try setting the memory manually. Please see 
http://code.google.com/p/peptide-shaker/issues/detail?id=87#c1 for more details.

Original comment by harald.b...@gmail.com on 12 Jul 2015 at 11:39

hbarsnes commented 8 years ago

This issue was solved in later versions of the library. If this is not the case, please let us know and we'll reopen the issue.