Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Won't Fix
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Labels:None
Description
Before we do a new release, check the "zip" files from Sourceforge and our server. We link to them from the download page.
Two key things to check:
- the zip file is updated and has the latest version
- When you unpack the zip file, you can run IGB it by double-clicking the script file (scripts should be executable)
Please retest ON release day!!
Attachments
Issue Links
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- Closed
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Activity
This also happens on my Mac 10.7.5 with both Java 1.6 & 1.7, but not Mac 10.6.8
There are several similar errors on Internet:
http://forum.processing.org/topic/java-errors
https://discussions.apple.com/message/18394472#18394472
Can you please check if this happens on your environment?
download of zip from our download page OR from sourceforge... all open IGB, but all terminal windows show the following (see several errors at the end)
Feb 25, 2013 10:15:17 AM com.affymetrix.igb.util.StatusBarOutput initStatusBarOutput
INFO: Initializing statusbar output messages
Feb 25, 2013 10:15:17 AM com.affymetrix.igb.prefs.WebLink autoLoad
INFO: Loading web links from file "/Users/auser/.igb/weblinks.xml"
Feb 25, 2013 10:15:18 AM com.affymetrix.igb.stylesheet.XmlStylesheetParser getSystemStylesheet
INFO: Loading system stylesheet from resource:/igb_system_stylesheet.xml
Feb 25, 2013 10:15:18 AM com.affymetrix.igb.stylesheet.XmlStylesheetParser getUserStylesheet
INFO: Loading user stylesheet from resource: user_stylesheet.xml
Feb 25, 2013 10:15:19 AM com.affymetrix.genometryImpl.das.DasServerInfo getInputStream
INFO: Das Request : http://bioviz.org/cached/UCSCDas//dsn.xml
DAS server version: , status:
DAS capabilities:
Feb 25, 2013 10:15:19 AM com.affymetrix.genometryImpl.das2.Das2ServerInfo getInputStream
INFO: Loading from server : http://bioviz.org/das2/genome
Initializing http://bioviz.org/das2/genome
Feb 25, 2013 10:15:19 AM com.affymetrix.genometryImpl.util.LocalUrlCacher loadSynonyms
INFO: Synonyms found at: http://igbquickload.org/quickload/synonyms.txt
Feb 25, 2013 10:15:19 AM com.affymetrix.genometryImpl.das2.Das2ServerInfo getInputStream
INFO: Loading from server : http://igbquickload.org/das2/genome
Initializing http://igbquickload.org/das2/genome
Feb 25, 2013 10:15:20 AM com.affymetrix.igb.tutorial.Activator loadDefaultTutorialPrefs
INFO: loading default tutorial preferences from: /tutorial_default_prefs.xml
Feb 25, 2013 10:15:20 AM com.affymetrix.igb.bookmarks.SimpleBookmarkServer findAvailablePort
INFO: Found available port for bookmark server: 7,085
Feb 25, 2013 10:15:20 AM com.affymetrix.igb.bookmarks.action.BookmarkActionManager addDefaultBookmarks
INFO: Loading bookmarks from file /Users/auser/.igb/bookmarks.html
Feb 25, 2013 10:15:20 AM com.affymetrix.main.OSGiHandler startOSGi
INFO: OSGi is started with org.apache.felix.framework version 4.0.1
Feb 25 10:15:21 phoebe.local java[38912] <Error>: CGContextGetCTM: invalid context 0x0
Feb 25 10:15:21 phoebe.local java[38912] <Error>: CGContextSetBaseCTM: invalid context 0x0
Feb 25 10:15:21 phoebe.local java[38912] <Error>: CGContextGetCTM: invalid context 0x0
Feb 25 10:15:21 phoebe.local java[38912] <Error>: CGContextSetBaseCTM: invalid context 0x0
According to those posting the error is due to OS. So it won't be fixed.