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  1. IGB
  2. IGBF-2433

Check build on Debian

        Details

        • Type: Documentation
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Earlier in the month we received a notification from a user that IGB was failing to build on a Debian system.

          Turns out the problem was lack of JavaFX on the system.

          To make sure others do not encounter the same problem, we should check into this a bit more. Let's clarify which versions of Java can be installed using Debian package managers versus having to download them from Oracle. Let's summarize what we find here (in this ticket) and then update the README.md on the IGB repository.

          See:

          https://groups.google.com/forum/#!topic/integrated-genome-browser-help-desk/B5ReR-c_Po8

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              Issue Links

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              Task - A task that needs to be done. IGBF-2459 Post to Developers Group explaining how to build on Debian

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Chester Dias [ cdias1 ]
                ann.loraine Ann Loraine made changes -
                Assignee Chester Dias [ cdias1 ] Chaitanya Kintali [ chaitanya ]
                ann.loraine Ann Loraine made changes -
                Assignee Chaitanya Kintali [ chaitanya ]
                cdias1 Chester Dias (Inactive) made changes -
                Assignee Chester Dias [ cdias1 ]
                cdias1 Chester Dias (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                cdias1 Chester Dias (Inactive) added a comment -

                Cause of error and failure in build occurred due to below issue
                igb-javafx-util: Compilation failure

                This package needs java fx to be present

                Testing is done on Debian 9(Stretch) using Maven: 3.6.3
                Installation of oracle java was not successful on this OS with the default packages link showing 404 error in the apt installer.
                Alternatively, I used the openjdk8 installation

                sudo apt-get update
                sudo apt update
                sudo apt-get install openjdk-8-jdk

                This package does not have javafx by default and has to be installed seperately using below command

                sudo apt-get install openjfx

                This builds the application successfully. Attached is the build details from the Debian 9 OS

                Debian 10 does not seem to have openjdk available in its default repositories.
                Below are the steps to install oracle java jdk on Debian 10.Note to the user: Ensure the right architecture package is used (either X64 java for 64 bit OS and X86 for a 32 bit OS)
                Step 1. Download the correct Java from https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html

                sudo mkdir -p /usr/lib/jvm
                sudo tar -zxvf jdk-8u251-linux-x64.tar.gz -C /usr/lib/jvm/
                sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk1.8.0_251/bin/java 1

                This built IGB successfully on Debian 10(Buster)

                [~aloraine] Please let me know if I should update the README.md to include the steps

                Show
                cdias1 Chester Dias (Inactive) added a comment - Cause of error and failure in build occurred due to below issue igb-javafx-util: Compilation failure This package needs java fx to be present Testing is done on Debian 9(Stretch) using Maven: 3.6.3 Installation of oracle java was not successful on this OS with the default packages link showing 404 error in the apt installer. Alternatively, I used the openjdk8 installation sudo apt-get update sudo apt update sudo apt-get install openjdk-8-jdk This package does not have javafx by default and has to be installed seperately using below command sudo apt-get install openjfx This builds the application successfully. Attached is the build details from the Debian 9 OS Debian 10 does not seem to have openjdk available in its default repositories. Below are the steps to install oracle java jdk on Debian 10.Note to the user: Ensure the right architecture package is used (either X64 java for 64 bit OS and X86 for a 32 bit OS) Step 1. Download the correct Java from https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html sudo mkdir -p /usr/lib/jvm sudo tar -zxvf jdk-8u251-linux-x64.tar.gz -C /usr/lib/jvm/ sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk1.8.0_251/bin/java 1 This built IGB successfully on Debian 10(Buster) [~aloraine] Please let me know if I should update the README.md to include the steps
                Hide
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                cdias1 Chester Dias (Inactive) added a comment -

                Also note
                Oracle java contains JavaFX by default
                openjdk needs an additional package to be installed

                All test performed above were on fresh Debian OS versions 9, 10

                Show
                cdias1 Chester Dias (Inactive) added a comment - Also note Oracle java contains JavaFX by default openjdk needs an additional package to be installed All test performed above were on fresh Debian OS versions 9, 10
                cdias1 Chester Dias (Inactive) made changes -
                Attachment Build logs [ 14770 ]
                cdias1 Chester Dias (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                cdias1 Chester Dias (Inactive) made changes -
                Assignee Chester Dias [ cdias1 ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Chester Dias [ cdias1 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-2459 [ IGBF-2459 ]

                  People

                  • Assignee:
                    cdias1 Chester Dias (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: