Can Java be uninstalled or upgraded on a MassLynx PC? - WKB13796

ENVIRONMENT

• MassLynx
• Java 5 (J2SE Runtime Environment 5.0)

ANSWER

Java 5 (jre1.5.0_17) is a prerequisite for MassLynx 4.1 and 4.2. When MassLynx is installed, the installer determines if Java 5 is present; if it's not, Java 5 is installed. However, Java 5 is needed only for the display of .mol files. If this functionality is not needed, Java 5 can be uninstalled or upgraded, as follows:

Uninstallation of Java 5

Java 5 can be uninstalled, provided that the existing MMMolViewer.jar and WMFWriter.jar files (located in the Java 5 folder at C:\Program Files(x86)\Java\jre1.5.0_17\lib\ext) are not deleted. MassLynx creates these two files during installation. Because they are not installed by Java, they are not removed when Java is uninstalled via Control Panel > Programs and Features. However, the Java 5 folder must not be manually deleted.

Upgrading the Java version

If MassLynx is already installed:

1. Install the new version of Java (for example, Java 8).
2. Copy the existing MMMolViewer.jar and WMFWriter.jar files from C:\Program Files(x86)\Java\jre1.5.0_17\lib\ext to the new Java folder (for Java 8, for example, it would be C:\Program Files(x86)\Java\jre1.8.0_131\lib\ext).
3. Uninstall Java 5, and then delete the Java 5 folder.

If MassLynx if not already installed

1. Install the new version of Java (for example, Java 8).
2. Install MassLynx.
3. Uninstall Java 5 (which was just installed by MassLynx), and then delete the Java 5 folder.

In this case, the MMMolViewer.jar and WMFWriter.jar files are installed by MassLynx in the Java 8 folder.

Important: If you use the Molecular Structure Viewer in the MetaboLynx browser, Java is required, and the Java version should be left at version 5.

ADDITIONAL INFORMATION

If the user deletes the Java 5 folder, including the MMMolViewer.jar and WMFWriter.jar files, before upgrading Java, MassLynx will display the following warning at startup:

Please wait while Windows configures MassLynx V4.1 SCN XXX’.

MassLynx then locates the original MassLynx installation files, reinstalls the MMMolViewer.jar and WMFWriter.jar in the new Java folder, and runs the IQ checker. It is then possible to start MassLynx normally.

If MassLynx cannot find the original source files, the user has the opportunity to manually browse to a new location of the MassLynx installation files.

However, if the MassLynx installation has been patched (for example with SCN 945 + SCN 960), this process fails, and MassLynx is unable to reinstall the required Java files. In this case, the MMMolViewer.jar and WMFWriter.jar files (attached) must be manually copied to the required subfolder of the new Java folder.

Note:Java has been removed from MassLynx 4.2 SCN 1024 basic installation for the Xevo TQD, Xevo TQ-S micro and Xevo TQ-XS.

Java will no longer be present in future MassLynx SCNs except where required in Application managers (ChromaLynx and OpenLynx Browser molecule display)