Hi Syed, I can ping to www.biomart.org. I got the same connection time out error when trying "Relational Mart" or "Database Schema".
Thank you in advance for your help Yue Syed Haider <[email protected]> 02/21/2011 01:42 PM To Yue W Webster <[email protected]> cc Arek Kasprzyk <[email protected]>, "[email protected]" <[email protected]>, Jian WJ Wang <[email protected]> Subject Re: [BioMart Users] problem installing biomart Hi Yue, Can you connect (ping/wget) to www.biomart.org from the machine you are running MartConfigurator ? Also, what happens when you try 'Relational Mart' option instead of 'URL Mart'? Syed On 21/02/2011 17:54, Yue W Webster wrote: > > Hello Arek, > > Jian and I are trying to install biomart on one of our Linux server. We followed instructions in ?BioMart 0.8 User Manual, release candidate 4, 1st February 2010?. We were able to complete step 1-4(START MARTCONFIGURATOR). On step 5, we were able to open ?Add Data Source? window, but when we clicked the Get? button, none of the available marts appear in the left panel (see following picture). Could you help? > [cid:_1_0B293AB40B2936F8006267E48525783E] > > After a while, we got a Java time out error on the Linux command line window: > java.net.ConnectException: Connection timed out > at java.net.PlainSocketImpl.socketConnect(Native Method) > at java.net.PlainSocketImpl.doConnect(Unknown Source) > at java.net.PlainSocketImpl.connectToAddress(Unknown Source) > at java.net.PlainSocketImpl.connect(Unknown Source) > at java.net.Socket.connect(Unknown Source) > at java.net.Socket.connect(Unknown Source) > at sun.net.NetworkClient.doConnect(Unknown Source) > at sun.net.www.http.HttpClient.openServer(Unknown Source) > at sun.net.www.http.HttpClient.openServer(Unknown Source) > at sun.net.www.http.HttpClient.<init>(Unknown Source) > at sun.net.www.http.HttpClient.New(Unknown Source) > at sun.net.www.http.HttpClient.New(Unknown Source) > at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source) > at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) > at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source) > at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) > at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source) > at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) > at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) > at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453) > at org.jdom.input.SAXBuilder.build(SAXBuilder.java:810) > at org.biomart.configurator.utils.McGuiUtils.getMartsFromURL(McGuiUtils.java:563) > at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.setUrlMetaTree(DataLinkDialog.java:425) > at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.access$1100(DataLinkDialog.java:61) > at org.biomart.configurator.view.gui.dialogs.DataLinkDialog$4.actionPerformed(DataLinkDialog.java:377) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.Dialog$1.run(Unknown Source) > at java.awt.Dialog$3.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.awt.Dialog.show(Unknown Source) > at java.awt.Component.show(Unknown Source) > at java.awt.Component.setVisible(Unknown Source) > at java.awt.Window.setVisible(Unknown Source) > at java.awt.Dialog.setVisible(Unknown Source) > at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.showDialog(DataLinkDialog.java:75) > at org.biomart.configurator.controller.ObjectController.addMarts(ObjectController.java:79) > at org.biomart.configurator.view.idwViews.McViewSourceTree.mousePressed(McViewSourceTree.java:248) > at java.awt.AWTEventMulticaster.mousePressed(Unknown Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > > > our server is running Linux X86_64 > > Thank you for your help >
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