Error Upgrading

[infrontsoftware]

I am attempting to upgrade to 6.15.3 (from 6.7.2) on a hosted server after having been infected by the WebDAV/Widget Connector vulnerability intrusion described in the 2019-03-20 security notice.

I believe I have the malware cleaned up and am working on the upgrade now to fix the vulnerability.

I downloaded 6.15.3 from https://www.atlassian.com/software/confluence/download?_ga=2.44997348.1718723340.1556293474-277659931.1556037557 for Ubuntu.  

I followed instructions at https://confluence.atlassian.com/doc/upgrading-confluence-4578.html and when I attempt to 

sudo ./atlassian-confluence-6.15.3-x64.bin

I receive the following stack trace.   I need some guidance on how to resolve that issue.

Thanks!

Daniel

XXXXX:~/infront-files$ sudo ./atlassian-confluence-6.15.3-x64.binInstalling fontconfig...Hit:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial InReleaseGet:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB]Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [109 kB]         Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main Sources [335 kB]Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe Sources [254 kB]Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/multiverse Sources [8,764 B]Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [946 kB]Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [378 kB]Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 Packages [746 kB]Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe Translation-en [310 kB]Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 Packages [16.7 kB]Get:13 http://security.ubuntu.com/ubuntu xenial-security/main Sources [145 kB] Get:14 http://security.ubuntu.com/ubuntu xenial-security/universe Sources [105 kB]Get:15 http://security.ubuntu.com/ubuntu xenial-security/multiverse Sources [3,420 B]Get:16 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [638 kB]Get:17 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [261 kB]Get:18 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 Packages [434 kB]Get:19 http://security.ubuntu.com/ubuntu xenial-security/universe Translation-en [176 kB]Get:20 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 Packages [5,604 B]Fetched 5,087 kB in 1s (4,129 kB/s)                    Reading package lists... DoneBuilding dependency tree       Reading state information... Done149 packages can be upgraded. Run 'apt list --upgradable' to see them.E: dpkg was interrupted, you must manually run 'sudo dpkg --configure -a' to correct the problem. Unpacking JRE ...Starting Installer ...An error occurred:java.lang.RuntimeException: java.lang.reflect.InvocationTargetExceptionError log: /tmp/install4jError4277272808087349687.logjava.lang.RuntimeException: java.lang.reflect.InvocationTargetException at com.install4j.runtime.installer.frontend.GUIHelper.invokeOnEDT(GUIHelper.java:703) at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.init(AbstractHeadlessScreenExecutor.java:73) at com.install4j.runtime.installer.frontend.headless.ConsoleScreenExecutor.<init>(ConsoleScreenExecutor.java:24) at com.install4j.runtime.installer.frontend.headless.InstallerConsoleScreenExecutor.<init>(InstallerConsoleScreenExecutor.java:6) at com.install4j.runtime.installer.Installer.getScreenExecutor(Installer.java:87) at com.install4j.runtime.installer.Installer.runInProcess(Installer.java:56) at com.install4j.runtime.installer.Installer.main(Installer.java:45) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:85) at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:62)Caused by: java.lang.reflect.InvocationTargetException at java.awt.EventQueue.invokeAndWait(EventQueue.java:1349) at java.awt.EventQueue.invokeAndWait(EventQueue.java:1324) at com.install4j.runtime.installer.frontend.GUIHelper.invokeOnEDT(GUIHelper.java:699) ... 12 moreCaused by: java.lang.NullPointerException at sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1264) at sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:219) at sun.awt.FontConfiguration.init(FontConfiguration.java:107) at sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:774) at sun.font.SunFontManager$2.run(SunFontManager.java:431) at java.security.AccessController.doPrivileged(Native Method) at sun.font.SunFontManager.<init>(SunFontManager.java:376) at sun.awt.FcFontManager.<init>(FcFontManager.java:35) at sun.awt.X11FontManager.<init>(X11FontManager.java:57) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at java.lang.Class.newInstance(Class.java:442) at sun.font.FontManagerFactory$1.run(FontManagerFactory.java:83) at java.security.AccessController.doPrivileged(Native Method) at sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74) at sun.font.SunFontManager.getInstance(SunFontManager.java:250) at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264) at sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:1113) at javax.swing.JComponent.getFontMetrics(JComponent.java:1626) at javax.swing.text.WrappedPlainView.updateMetrics(WrappedPlainView.java:318) at javax.swing.text.WrappedPlainView.updateChildren(WrappedPlainView.java:297) at javax.swing.text.WrappedPlainView.insertUpdate(WrappedPlainView.java:463) at javax.swing.plaf.basic.BasicTextUI$RootView.insertUpdate(BasicTextUI.java:1610) at javax.swing.plaf.basic.BasicTextUI$UpdateHandler.insertUpdate(BasicTextUI.java:1869) at javax.swing.text.AbstractDocument.fireInsertUpdate(AbstractDocument.java:201) at javax.swing.text.AbstractDocument.handleInsertString(AbstractDocument.java:748) at javax.swing.text.AbstractDocument.insertString(AbstractDocument.java:707) at javax.swing.text.PlainDocument.insertString(PlainDocument.java:130) at javax.swing.text.DefaultEditorKit.read(DefaultEditorKit.java:273) at javax.swing.JEditorPane.setText(JEditorPane.java:1416) at javax.swing.JEditorPane.<init>(JEditorPane.java:290) at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.createEditorPane(AbstractHeadlessScreenExecutor.java:357) at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.initFontManager(AbstractHeadlessScreenExecutor.java:309) at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.access$400(AbstractHeadlessScreenExecutor.java:28) at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor$2.run(AbstractHeadlessScreenExecutor.java:77) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:301) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

[infrontsoftware · Accepted solution]

I resolved this particular issue.

To those who find this later, I needed to execute 

   sudo dpkg --configure -a

And then subsequently 

  sudo apt-get -f install