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Valentin Georgiev valyo

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@valyo
valyo / Using the GUI
Created January 10, 2012 13:16
Generate 3D... > Balloon
14:02:47.675 INFO [n.bioclipse.balloon.runner.BalloonRunner] Running 'balloon -c 1 /Users/valentingeorgiev/bioclipse-workspace/screenU251new/screen_U251.sdf /Users/valentingeorgiev/bioclipse-workspace/screenU251new/screen_U251_3d_3.mdl
14:02:47.675 INFO [net.sf.jnati.proc.ProcessMonitor] Executing command: /Users/valentingeorgiev/dev/bioclipse/bioclipse.balloon/plugins/net.bioclipse.balloon.macosx/exec/balloon
14:12:47.677 WARN [net.sf.jnati.proc.ProcessMonitor] Timed-out: cancelling command (600002ms)
14:12:47.680 INFO [net.sf.jnati.proc.ProcessMonitor] Interrupted: destroying process
14:12:47.682 INFO [net.sf.jnati.proc.StreamGobbler] Interrupted: stopping
14:12:47.682 INFO [net.sf.jnati.proc.StreamGobbler] Interrupted: stopping
14:12:47.685 ERROR [n.b.balloon.handlers.BalloonGen3DHandler] Balloon failed: Balloon timed out. Reason: null
!ENTRY net.bioclipse.balloon.business 4 0 2012-01-10 14:12:47.687
!MESSAGE Balloon failed: Balloon timed out. Reason: null
@valyo
valyo / Using Bioclipse Scripting Language
Created January 10, 2012 12:19
mols=cdk.loadSMILESFile("/U251/screen_U251.smi");
10:35:54.763 DEBUG [net.bioclipse.cdk.business.CDKManager] Number of lines in file: 3744
10:35:54.764 DEBUG [net.bioclipse.cdk.business.CDKManager] Header line is: smiles name class
10:36:06.739 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 35 due to failed atom typing.
10:36:06.818 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 73 due to failed atom typing.
10:36:08.858 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 99 due to failed atom typing.
10:36:13.305 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 155 due to failed atom typing.
10:37:29.589 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 202 due to failed atom typing.
10:37:30.845 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 217 due to failed atom typing.
10:37:30.847 DEBUG [net.bioclipse.cdk.business.CDKManager] Skipped molecule 218 due to failed atom typing.
10:39:10.932 ERROR [net.bioclipse.cdk.business.CDKManager] Could not deduce bond orders for mol:
@valyo
valyo / gist:1399735
Created November 28, 2011 09:19
bioclipse.cheminformatics installation
Cannot complete the install because of a conflicting dependency.
Software being installed: Bioclipse Chemoinformatics 2.5.0.201109121822 (net.bioclipse.chemoinformatics_feature.feature.group 2.5.0.201109121822)
Software currently installed: Bioclipse 2.5.0.qualifier (net.bioclipse.product 2.5.0.qualifier)
Only one of the following can be installed at once:
Bioclipse Core 2.5.0.201110071324 (net.bioclipse.core 2.5.0.201110071324)
Bioclipse Core 2.5.0.201109090726 (net.bioclipse.core 2.5.0.201109090726)
Bioclipse Core 2.5.0.201107061021 (net.bioclipse.core 2.5.0.201107061021)
Cannot satisfy dependency:
From: Bioclipse Chemoinformatics 2.5.0.201109121822 (net.bioclipse.chemoinformatics_feature.feature.group 2.5.0.201109121822)
@valyo
valyo / pharmbio
Created November 18, 2011 14:09
latex output
valentin:book valentingeorgiev$ latexmk -pdf -pvc pharmbio.tex
Latexmk: This is Latexmk, John Collins, 7 May 2011, version: 4.24.
**** Report bugs etc to John Collins <collins at phys.psu.edu>. ****
Viewing pdf
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': File changes, etc:
Non-existent destination files:
'pharmbio.pdf'
------------
Run number 1 of rule 'pdflatex'
@valyo
valyo / .log
Created October 28, 2011 16:01
BC2.5/openSUSE 32-bit
!SESSION 2011-11-14 15:15:34.901 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_22
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os linux -ws gtk -arch x86 -data @nodefault -noupdate -consolelog
!ENTRY org.eclipse.core.resources 2 10035 2011-11-14 15:15:36.356
!MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
@valyo
valyo / .log
Created October 26, 2011 10:51
BC2.5/Ubuntu 64bit - starting Bioclipse-R
!SESSION 2011-11-14 11:46:03.647 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_22
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os linux -ws gtk -arch x86_64 -data @nodefault -noupdate -consolelog
!ENTRY org.eclipse.core.resources 2 10035 2011-11-14 11:46:07.402
!MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
@valyo
valyo / Bioclipse log
Created October 25, 2011 15:58
Bioclipse log XP 32 bit
!SESSION 2011-10-25 11:26:50.989 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_29
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog
!ENTRY org.eclipse.core.resources 2 10035 2011-10-25 11:26:53.753
!MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
@valyo
valyo / Bioclipse log
Created October 25, 2011 15:49
Bioclipse log Vista 32 bit
!SESSION 2011-10-20 13:57:45.113 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_29
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog
!ENTRY org.eclipse.core.resources 2 10035 2011-10-20 13:57:50.051
!MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
@valyo
valyo / .log
Created October 24, 2011 14:54
BC 2.5/Vista - BC-R R does not start
!SESSION 2011-10-20 13:15:37.276 -----------------------------------------------
eclipse.buildId=2.5.0.201108060919
java.version=1.6.0_29
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Framework arguments: -noupdate
Command-line arguments: -os win32 -ws win32 -arch x86 -data @nodefault -noupdate -consolelog
!ENTRY de.walware.rj.servi 4 0 2011-10-20 13:15:55.928
!MESSAGE An exception was thrown when trying to start the node (make a node).
@valyo
valyo / BC Browser error log
Created October 21, 2011 11:58
BC2.5/Ubuntu Window->Show view->Other->General->Internal Web Browser
Embedded browser not available
Problem Details
The embedded browser widget for this editor cannot be created. It is either not available for your operating system or the system needs to be configured to support embedded browser
<<Details
No more handles [Unknown Mozilla path (MOZILLA_FIVE_HOME not set)]
org.eclipse.swt.SWTError: No more handles [Unknown Mozilla path (MOZILLA_FIVE_HOME not set)]
at org.eclipse.swt.SWT.error(SWT.java:4109)
at org.eclipse.swt.browser.Mozilla.initMozilla(Mozilla.java:1739)