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: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Epic Link:
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Sprint:Fall 7, Fall 8, Spring 1
Description
Situation: As part of the migration to JDK21 we are also updating the Docker image to use Install4J v10.
Task:
- Create the IGB Docker image used in Bitbucket pipeline to use Install4J v10 with our JRE bundles for Linux, Mac ARM (ARCH64), Mac Intel (AMD64), and Windows.
- Confirm that the Docker image can build installers using Bitbucket pipeline
- Update the documentation as required in the IGB Docker repository: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/
- Confirm that the new Dockerfile can properly create the Docker image using a Loraine Lab VM in AWS (see: https://bitbucket.org/lorainelab/bioviz-playbooks/src/master/docker.yml - note: this may also need updating and documentation)
- Once all of the above has been done, push our new Docker image to the Loraine Lab Docker hub account with the correct tag
Note that DCN has already created a Docker image which we've been testing with our Bitbucket pipeline.
Attachments
Issue Links
- relates to
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IGBF-3521 Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0
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Show 4 more links (4 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3142 [ 21688 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Situation: As part of the migration to JDK21 we are also updating the Docker image to use Install4J v10.
Task: Update the IGB Docker image to use Install4J v10. |
We looked into supporting Windows Arm laptops (surface), but we need a JDK21+FX Windows Arm JDK, and that doesn't seem to exist right now. There is an option in Install4Jv10 for supporting Windows Arm, but we're not sure how that would work since we can't provide/find the necessary JDK, and the JDKs that Install4J accesses don't seem to include FX.
Because we are not using two different installers for Mac we need to change the naming logic for Install4J to specify how the files are named. So we are now using the system architecture (i.e. Mac aarch64 for Arm) to differentiate the two files.
When configuring Install4J using the GUI, we need to make sure we exclude files from the installer that we don't need. We do need the installer, jar, and can also include notices, readme, license, code of conduct.
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 7 [ 183 ] | Fall 7, Fall 8 [ 183, 184 ] |
| Rank | Ranked higher |
This task is mostly complete. Sub-tasks I would like to see complete before closing this ticket are:
- Stop skipping tests in build DONE
- Update Windows signing keys
- Why is installer so big (dmg went from 150MB to 350MB)
| Description |
Situation: As part of the migration to JDK21 we are also updating the Docker image to use Install4J v10.
Task: Update the IGB Docker image to use Install4J v10. |
Situation: As part of the migration to JDK21 we are also updating the Docker image to use Install4J v10.
Task: * Create the IGB Docker image used in Bitbucket pipeline to use Install4J v10 with our JRE bundles for Linux, Mac ARM (ARCH64), Mac Intel (AMD64), and Windows. * Confirm that the Docker image can build installers using Bitbucket pipeline * Update the documentation as required in the IGB Docker repository: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/ * Confirm that the new Dockerfile can properly create the Docker image using a Loraine Lab VM in AWS (see: https://bitbucket.org/lorainelab/bioviz-playbooks/src/master/docker.yml - note: this may also need updating and documentation) * Once all of the above has been done, push our new Docker image to the Loraine Lab Docker hub account with the correct tag Note that DCN has already created a Docker image which we've been testing with our Bitbucket pipeline. |
Update:
- David contributed a new branch "JDK21" to integrated-genome-browser-docker repo; new branch is: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/branch/jdk21
- I created a new VM using the AWS interface - it uses the new Amazon "AMI 2023" image configured with 2 Gb RAM and 24 Gb storage
- I used a playbook (docker.yml in the "bioviz.org" repo) to install docker and other stuff on it
- I cloned the IGB Docker repo onto the VM with: git clone https://aloraine@bitbucket.org/lorainelab/integrated-genome-browser-docker.git
- I checked out the new branch - JDK21
- Built a new docker image with:
docker build -t igb-maven-install4j:I4J10-jre-21.0.1 .
following instructions here: https://docs.aws.amazon.com/AmazonECS/latest/developerguide/create-container-image.html
Output from docker build command in the preceding comment:
docker.bioviz.org ec2-user $ docker build -t igb-maven-install4j:I4J10-jre-21.0.1 . [+] Building 285.8s (16/16) FINISHED docker:default => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 2.92kB 0.0s => [internal] load .dockerignore 0.1s => => transferring context: 151B 0.0s => [internal] load metadata for docker.io/library/ubuntu:jammy 0.7s => [internal] load build context 0.0s => => transferring context: 986B 0.0s => [builder 1/4] FROM docker.io/library/ubuntu:jammy@sha256:8eab65df3 2.3s => => resolve docker.io/library/ubuntu:jammy@sha256:8eab65df33a6de284 0.0s => => sha256:8eab65df33a6de2844c9aefd19efe8ddb87b7df5 1.13kB / 1.13kB 0.0s => => sha256:149d67e29f765f4db62aa52161009e99e389544e25a8 424B / 424B 0.0s => => sha256:b6548eacb0639263e9d8abfee48f8ac8b327102a 2.30kB / 2.30kB 0.0s => => sha256:5e8117c0bd28aecad06f7e76d4d3b64734d59c 29.55MB / 29.55MB 0.4s => => extracting sha256:5e8117c0bd28aecad06f7e76d4d3b64734d59c1a0a445 1.7s => [builder 2/4] RUN apt-get update && apt-get install -y curl 16.5s => [stage-1 2/8] RUN apt-get update && apt-get install -y curl 18.6s => [builder 3/4] RUN curl -s "https://get.sdkman.io" | bash 2.7s => [builder 4/4] RUN source "$HOME/.sdkman/bin/sdkman-init.sh" && 101.0s => [stage-1 3/8] COPY --from=builder /root/.sdkman /root/.sdkman 0.3s => [stage-1 4/8] COPY settings.xml /root/.m2/settings.xml 0.0s => [stage-1 5/8] RUN curl -o install4j.deb https://download.ej-techn 21.4s => [stage-1 6/8] RUN curl -Lo windows-amd64-21.0.1.tar.gz https://bi 50.2s => [stage-1 7/8] RUN mkdir -p /root/.local/share/install4j/v10/jres/ 15.6s => [stage-1 8/8] RUN rm -rf /opt/install4j10/jre 0.5s => exporting to image 59.5s => => exporting layers 59.5s => => writing image sha256:2e7cb3f63270f62c56c8a3436aa0647b24a04936b8 0.0s => => naming to docker.io/library/igb-maven-install4j:I4J10-jre-21.0. 0.0s docker.bioviz.org ec2-user $
After building the Docker image (see preceding comment), made a "build" directory and cloned David's IGB fork branch JDK21 into it with:
cd
mkdir ./build
git clone --single-branch --branch main-JDK21 https://bitbucket.org/hillrunner2008/integrated-genome-browser build/.
Confirmed the new Docker image is available:
docker.bioviz.org ec2-user $ docker images REPOSITORY TAG IMAGE ID CREATED SIZE igb-maven-install4j I4J10-jre-21.0.1 2e7cb3f63270 9 minutes ago 4.12GB
Attempted to run the docker image with:
docker run -i -t -v ~/build:/build --workdir /build igb-maven-install4j:I4J10-jre-21.0.1
However, there was an error:
[INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.194 s [INFO] Finished at: 2023-12-12T22:19:38Z [INFO] ------------------------------------------------------------------------ [ERROR] No goals have been specified for this build. You must specify a valid lifecycle phase or a goal in the format <plugin-prefix>:<goal> or <plugin-group-id>:<plugin-artifact-id>[:<plugin-version>]:<goal>. Available lifecycle phases are: pre-clean, clean, post-clean, validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy, pre-site, site, post-site, site-deploy. -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/NoGoalSpecifiedException
I think this is because the docker image runs a command (mvn) when it is "run", due to the final command in the docker file.
To run the image interactively and not have it automatically try to execute that final command, I need to run give it a command to run that will override the "mvn" command.
I did this with:
docker run -i -t -v ~/build:/build --workdir /build igb-maven-install4j:I4J10-jre-21.0.1 /bin/bash
The above command "dumped" me into the docker image itself. I then proceeded to the next step, with:
mvn install
This built "igb_exe.jar" as expected. However, there were a number of warnings. I made note of one of them in multiple new tickets, all linked to this ticket. I also am attaching the stdout and stderr from "mvn install".
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked lower |
| Attachment | a0860834e-mvn-install-stdout.txt [ 18154 ] | |
| Attachment | a0860834e-mvn-install-stderr.txt [ 18155 ] |
For next step,
- created env_vars environment variables file (with license key and other info needed by the installer build process)
- deployed files used to sign Windows and Mac jars onto EC2
- re-started the docker image with:
docker run -i -t -v ~/build:/build --env-file env_vars --workdir /build igb-maven-install4j:I4J10-jre-21.0.1 /bin/bash
Tested installer build with:
mvn install -P release-bitbucket-pipelines
Installers were built and placed in directory /build/main/target/media. Installer files:
root@782c43f23bf4:/build/main/target/media# ls -lh total 1.2G -rw-r--r--. 1 root root 175M Dec 13 17:51 IGB-linux-amd64-10.0.0.sh -rw-r--r--. 1 root root 345M Dec 13 17:55 IGB-macos-aarch64-10.0.0.dmg -rw-r--r--. 1 root root 353M Dec 13 17:53 IGB-macos-amd64-10.0.0.dmg -rw-r--r--. 1 root root 346M Dec 13 17:50 IGB-windows-amd64-10.0.0.exe -rw-r--r--. 1 root root 247 Dec 13 17:55 md5sums -rw-r--r--. 1 root root 429 Dec 13 17:55 output.txt -rw-r--r--. 1 root root 375 Dec 13 17:55 sha256sums -rw-r--r--. 1 root root 1.8K Dec 13 17:55 updates.xml
Decided to push the newly built image to docker hub after renameing/re-tagging it, with:
docker tag 2e7cb3f63270 lorainelab/igb-maven-install4j:I4J10-nonuniversal-full-jre-21.0.1
To upload the new image to docker hub, first logged into docker hub with:
docker login -u aloraine
Next, attempted to push the new image with:
docker push lorainelab/igb-maven-install4j:I4J10-nonuniversal-full-jre-21.0.1
The new image is successfully uploaded - see:
Summary of work done thus far:
- A new Dockerfile is available on branch JDK21 in https://bitbucket.org/lorainelab/integrated-genome-browser-docker/src/master/
- An image built using the above Dockerfile is now available as lorainelab/igb-maven-install4j:I4J10-nonuniversal-full-jre-21.0.1 on docker hub
- Before push the new image to docker hub, I confirmed that I could build igb installers using the new image in an interactive sessions on an EC2 VM (Amazon AMI 2023)
To review / test :
- Confirm that you can build IGB installers in bitbucket pipelines on main-JDK21, the latest version of it available from hillrunner2008's fork
- To do this, fork his repo, make a branch, edit the bitbucket.yml file to use the lorainelab image, and then push your branch to your fork to trigger pipeline
- Check that you can run the "release" pipeline and the branch pipeline
If all is good, move to Done.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
Need to make new Docker image using newly created JRE bundles.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] |
Pull request from David: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/pull-requests/9
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 7, Fall 8 [ 183, 184 ] | Fall 7, Fall 8, Spring 1 [ 183, 184, 185 ] |
| Rank | Ranked higher |
Update:
- PR is merged is now merged. Tip of the branch is commit hash 69bbb97
- Changed main branch setting for https://bitbucket.org/lorainelab/integrated-genome-browser-docker to be "JDK21" as I like the convention of naming branches after the deployed JVM and the main branch should now be the JDK21 branch
- As per Nowlan's post to the google group (see https://groups.google.com/g/integrated-genome-browser-help-desk/c/Lrf8jWitZ-o/m/Faj7NP_9AAAJ), our current release candidate is from the branch main-JDK21-with-javafx-no-theme
- The latest tip of that branch is on Nowlan's repository: https://bitbucket.org/nfreese/nowlanfork-igb/
- Looks like I built a new version of the Docker image two weeks ago (before the break):
docker.bioviz.org ec2-user $ docker images REPOSITORY TAG IMAGE ID CREATED SIZE igb-maven-install4j I4J10-jre-21.0.1 91f23d890b25 2 weeks ago 2.86GB lorainelab/igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 3 weeks ago 4.12GB igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 3 weeks ago 4.12GB
Testing what appears to be the newly created docker image, equipped with universal binaries.
Cloning latest tip of the IGB JDK21 "no theme" branch from NF's repository:
git clone --single-branch --branch main-JDK21-with-javafx-no-theme https://bitbucket.org/nfreese/nowlanfork-igb build
Starting interactive session with docker image igb-maven-install4j:I4J10-jre-21.0.1:
docker run -i -t -v ~/build:/build --env-file env_vars --workdir /build igb-maven-install4j:I4J10-jre-21.0.1 /bin/bash
Copied required jar-signing files to build/distribution, then ran inside the docker container:
mvn install -P release-bitbucket-pipelines
Confirmed the installers were built:
root@913be92b0691:/build# ls -lh main/target/media/ total 538M -rw-r--r--. 1 root root 171M Jan 9 18:35 IGB-linux-amd64-10.0.0.sh -rw-r--r--. 1 root root 205M Jan 9 18:37 IGB-macos-universal-10.0.0.dmg -rw-r--r--. 1 root root 163M Jan 9 18:34 IGB-windows-amd64-10.0.0.exe -rw-r--r--. 1 root root 188 Jan 9 18:37 md5sums -rw-r--r--. 1 root root 359 Jan 9 18:37 output.txt -rw-r--r--. 1 root root 284 Jan 9 18:37 sha256sums -rw-r--r--. 1 root root 1.4K Jan 9 18:37 updates.xml
Downloaded the IGB MacOS installer onto my local and ran it:
open IGB-macos-universal-10.0.0.dmg
The installer ran fine, but then, when it finished by trying to start IGB, I got an error about the application "quitting unexpectedly".
I saved the error report to a file and attached it to this ticket.
I then tried again to launch the new IGB 10.0.0. Again, the application quit without running.
Downloading and attempting to run the IGB installer made by Nowlan Freese, and mentioned on the google group mentioned above.
Attached the error report to this ticket, but for some reason, the report file does not contain everything I copied from the Apple crash window. Reporting the errors below.
| Attachment | 2023-01-09-error-report-appleOS.txt [ 18165 ] |
| Attachment | 2023-01-09-error-report-appleOS.txt [ 18165 ] |
| Attachment | docker-built-crash-report-igb10-2024-01-09-Apple.txt [ 18166 ] |
| Attachment | nfreese-fork-crash-report-igb10-2024-01-09-Apple.txt [ 18167 ] |
Reviewing the crash reports, it appears the problem is related to javafx libraries.
From the crash report from running NF's fork's version of IGB 10.0.0 and also the Docker-built version of IGB 10.0.0.
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libjfxwebkit.dylib 0x00000000a7ddef01 0xa511f000 + 46923521
1 libjfxwebkit.dylib 0x00000000a7be207c 0xa511f000 + 44839036
2 libjfxwebkit.dylib 0x00000000a7a90434 0xa511f000 + 43455540
3 libjfxwebkit.dylib 0x00000000a748fd61 0xa511f000 + 37162337
4 libjfxwebkit.dylib 0x00000000a779f883 0xa511f000 + 40372355
5 libjfxwebkit.dylib 0x00000000a6e68f46 JSEvaluateScript + 806
6 libjfxwebkit.dylib 0x00000000a5e6c8c7 0xa511f000 + 13949127
7 libjfxwebkit.dylib 0x00000000a51ed386 Java_com_sun_webkit_WebPage_twkExecuteScript + 86
8 ??? 0x000000001f15d980 0 + 521525632
9 ??? 0x000000001f159166 0 + 521507174
10 ??? 0x000000001f159166 0 + 521507174
11 ??? 0x000000001f159166 0 + 521507174
12 ??? 0x000000001f159362 0 + 521507682
...
My Apple Intel computer is running macOS Big Sur Version 11.7.10.
Based on the above issue, I suspect that something is wrongly configured in the "universal" binaries deployed in the Docker image. Possibly the attempt to create the universal binaries is in error, somehow?
Question for Nowlan Freese: Does the Apple IGB 10.0.0 version released in our latest installers run on Intel computers at all?
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
My branch installer is working and running on an Intel Mac with OS 13.6.3. However, this branch has not been thoroughly tested yet.
| Attachment | docker-built-crash-report-igb10-2024-01-09-Apple.txt [ 18166 ] |
| Attachment | nfreese-fork-crash-report-igb10-2024-01-09-Apple.txt [ 18167 ] |
NF advised me to see if my system can build and run IGB 10.0.0, the latest branch.
So, I deployed JDK 21 onto my local computer, setting JAVA_HOME by adding the following line to my bash_profile script:
export JAVA_HOME="/Users/aloraine/JDKs/zulu21.30.15-ca-fx-jdk21.0.1-macosx_x64"
Confirming I have the latest version of the target branch:
local aloraine$ git remote -v origin git@bitbucket.org:nfreese/nowlanfork-igb.git (fetch) origin git@bitbucket.org:nfreese/nowlanfork-igb.git (push) local aloraine$ git checkout main-JDK21-with-javafx-no-theme Branch 'main-JDK21-with-javafx-no-theme' set up to track remote branch 'main-JDK21-with-javafx-no-theme' from 'origin'. Switched to a new branch 'main-JDK21-with-javafx-no-theme' local aloraine$ git pull origin main-JDK21-with-javafx-no-theme From bitbucket.org:nfreese/nowlanfork-igb * branch main-JDK21-with-javafx-no-theme -> FETCH_HEAD Already up to date. 3ebd3651f5 (HEAD -> main-JDK21-with-javafx-no-theme, origin/main-JDK21-with-javafx-no-theme) rolling back temporary change 2b33417d15 fix for felix configuration not loading correctly after upgrade 671d2680e1 changing laf for windows as a workaround for the classloading issues related to jidesoft and Windows LAF 4f702ade2a pipeline updates for new macos universal package
Confirming I am using the correct JDK:
local aloraine$ which javac /Users/aloraine/JDKs/zulu21.30.15-ca-fx-jdk21.0.1-macosx_x64/bin/javac local aloraine$ which java /Users/aloraine/JDKs/zulu21.30.15-ca-fx-jdk21.0.1-macosx_x64/bin/java
I have built IGB using the JDK21 and attempted to run it on my local, with:
local aloraine$ ./run_igb.sh WARNING: package com.sun.java.swing.plaf.windows not in java.desktop WARNING: package sun.awt.windows not in java.desktop 14:14:17.043 [main] INFO com.affymetrix.main.Main - Starting OSGI container 14:14:17.057 [main] INFO com.affymetrix.main.OSGiHandler - Loading OSGi framework 14:14:17.315 [main] INFO com.affymetrix.main.OSGiHandler - Loading embedded OSGi bundles 14:14:17.712 [main] INFO com.affymetrix.main.OSGiHandler - loading FastInfoset-2.1.1.jar 14:14:17.749 [main] INFO com.affymetrix.main.OSGiHandler - loading affymetrix-common-10.0.0.jar 14:14:17.753 [main] INFO com.affymetrix.main.OSGiHandler - loading annotation-tab-10.0.0.jar 14:14:17.756 [main] INFO com.affymetrix.main.OSGiHandler - loading apollo-library-10.0.0.jar 14:14:17.758 [main] INFO com.affymetrix.main.OSGiHandler - loading appstore-10.0.0.jar 14:14:17.761 [main] INFO com.affymetrix.main.OSGiHandler - loading bai-10.0.0.jar 14:14:17.764 [main] INFO com.affymetrix.main.OSGiHandler - loading bam-10.0.0.jar 14:14:17.767 [main] INFO com.affymetrix.main.OSGiHandler - loading bed-10.0.0.jar 14:14:17.769 [main] INFO com.affymetrix.main.OSGiHandler - loading bigBedHandler-10.0.0.jar 14:14:17.772 [main] INFO com.affymetrix.main.OSGiHandler - loading bigWigHandler-10.0.0.jar 14:14:17.775 [main] INFO com.affymetrix.main.OSGiHandler - loading bigwig-2.0.1.jar 14:14:17.779 [main] INFO com.affymetrix.main.OSGiHandler - loading bookmark-10.0.0.jar 14:14:17.783 [main] INFO com.affymetrix.main.OSGiHandler - loading cache-10.0.0.jar 14:14:17.786 [main] INFO com.affymetrix.main.OSGiHandler - loading cache-api-10.0.0.jar 14:14:17.792 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-codec-1.15.jar 14:14:17.801 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-compress-1.23.0.jar 14:14:17.803 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-csv-1.10.0.jar 14:14:17.806 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-fileupload-1.5.jar 14:14:17.810 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-io-2.11.0.jar 14:14:17.814 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-jexl-2.1.1.jar 14:14:17.819 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-lang3-3.12.0.jar 14:14:17.821 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-logging-1.2.jar 14:14:17.824 [main] INFO com.affymetrix.main.OSGiHandler - loading commons-pool-1.6.jar 14:14:17.826 [main] INFO com.affymetrix.main.OSGiHandler - loading console-tab-10.0.0.jar 14:14:17.829 [main] INFO com.affymetrix.main.OSGiHandler - loading context-menu-service-10.0.0.jar 14:14:17.831 [main] INFO com.affymetrix.main.OSGiHandler - loading das-10.0.0.jar 14:14:17.834 [main] INFO com.affymetrix.main.OSGiHandler - loading external-sort-10.0.0.jar 14:14:17.837 [main] INFO com.affymetrix.main.OSGiHandler - loading externalView-10.0.0.jar 14:14:17.839 [main] INFO com.affymetrix.main.OSGiHandler - loading failureaccess-1.0.1.jar 14:14:17.841 [main] INFO com.affymetrix.main.OSGiHandler - loading feedback-10.0.0.jar 14:14:17.843 [main] INFO com.affymetrix.main.OSGiHandler - loading frameManager-10.0.0.jar 14:14:17.852 [main] INFO com.affymetrix.main.OSGiHandler - loading genometry-10.0.0.jar 14:14:17.854 [main] INFO com.affymetrix.main.OSGiHandler - loading genotyping-10.0.0.jar 14:14:17.861 [main] INFO com.affymetrix.main.OSGiHandler - loading genoviz-1.1.9.jar 14:14:17.863 [main] INFO com.affymetrix.main.OSGiHandler - loading graphTab-10.0.0.jar 14:14:17.867 [main] INFO com.affymetrix.main.OSGiHandler - loading gson-2.10.1.jar 14:14:17.886 [main] INFO com.affymetrix.main.OSGiHandler - loading guava-32.1.1-jre.jar 14:14:17.888 [main] INFO com.affymetrix.main.OSGiHandler - loading heatmap-editor-10.0.0.jar 14:14:17.902 [main] INFO com.affymetrix.main.OSGiHandler - loading htsjdk-igb-3.0.5.jar 14:14:17.927 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-10.0.0.jar 14:14:17.949 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-genoviz-extensions-10.0.0.jar 14:14:17.952 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-javafx-util-10.0.0.jar 14:14:17.954 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-preferences-10.0.0.jar 14:14:17.956 [main] INFO com.affymetrix.main.OSGiHandler - loading igb-services-10.0.0.jar 14:14:17.958 [main] INFO com.affymetrix.main.OSGiHandler - loading igbScript-10.0.0.jar 14:14:17.960 [main] INFO com.affymetrix.main.OSGiHandler - loading igbSwingExt-10.0.0.jar 14:14:17.962 [main] INFO com.affymetrix.main.OSGiHandler - loading image-exporter-10.0.0.jar 14:14:17.965 [main] INFO com.affymetrix.main.OSGiHandler - loading istack-commons-runtime-4.2.0.jar 14:14:17.968 [main] INFO com.affymetrix.main.OSGiHandler - loading jakarta.activation-api-2.1.2.jar 14:14:17.971 [main] INFO com.affymetrix.main.OSGiHandler - loading jakarta.xml.bind-api-4.0.1.jar 14:14:17.974 [main] INFO com.affymetrix.main.OSGiHandler - loading jaxb-core-4.0.1.jar 14:14:17.982 [main] INFO com.affymetrix.main.OSGiHandler - loading jaxb-runtime-4.0.1.jar 14:14:18.026 [main] INFO com.affymetrix.main.OSGiHandler - loading jide-ultimate-jakarta-3.5.15.jar 14:14:18.028 [main] INFO com.affymetrix.main.OSGiHandler - loading keyWordSearch-10.0.0.jar 14:14:18.031 [main] INFO com.affymetrix.main.OSGiHandler - loading keybinding-registry-10.0.0.jar 14:14:18.035 [main] INFO com.affymetrix.main.OSGiHandler - loading logback-classic-1.2.12.jar 14:14:18.040 [main] INFO com.affymetrix.main.OSGiHandler - loading logback-core-1.2.12.jar 14:14:18.042 [main] INFO com.affymetrix.main.OSGiHandler - loading logging-config-10.0.0.jar 14:14:18.044 [main] INFO com.affymetrix.main.OSGiHandler - loading narrowpeak-10.0.0.jar 14:14:18.047 [main] INFO com.affymetrix.main.OSGiHandler - loading ncbiBlast-10.0.0.jar 14:14:18.051 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.bundlerepository-2.0.10.jar 14:14:18.054 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.configadmin-1.9.26.jar 14:14:18.058 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.eventadmin-1.6.4.jar 14:14:18.061 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.base-5.1.2.jar 14:14:18.084 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.jetty-5.1.4.jar 14:14:18.090 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.http.servlet-api-2.1.0.jar 14:14:18.094 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.scr-2.2.6.jar 14:14:18.099 [main] INFO com.affymetrix.main.OSGiHandler - loading org.apache.felix.webconsole-4.8.8.jar 14:14:18.101 [main] INFO com.affymetrix.main.OSGiHandler - loading org.lorainelab.igb.menu.api-10.0.0.jar 14:14:18.104 [main] INFO com.affymetrix.main.OSGiHandler - loading org.osgi.service.component-1.5.1.jar 14:14:18.106 [main] INFO com.affymetrix.main.OSGiHandler - loading org.osgi.service.log-1.5.0.jar 14:14:18.108 [main] INFO com.affymetrix.main.OSGiHandler - loading org.osgi.util.function-1.2.0.jar 14:14:18.110 [main] INFO com.affymetrix.main.OSGiHandler - loading org.osgi.util.promise-1.3.0.jar 14:14:18.112 [main] INFO com.affymetrix.main.OSGiHandler - loading osgi-resource-locator-2.5.0-b42.jar 14:14:18.114 [main] INFO com.affymetrix.main.OSGiHandler - loading paired-data-preprocessor-10.0.0.jar 14:14:18.120 [main] INFO com.affymetrix.main.OSGiHandler - loading plugins-manager-10.0.0.jar 14:14:18.123 [main] INFO com.affymetrix.main.OSGiHandler - loading propertyView-10.0.0.jar 14:14:18.125 [main] INFO com.affymetrix.main.OSGiHandler - loading quickload-10.0.0.jar 14:14:18.127 [main] INFO com.affymetrix.main.OSGiHandler - loading restrictionSites-10.0.0.jar 14:14:18.129 [main] INFO com.affymetrix.main.OSGiHandler - loading searchModelIdOrProps-10.0.0.jar 14:14:18.131 [main] INFO com.affymetrix.main.OSGiHandler - loading searchView-10.0.0.jar 14:14:18.134 [main] INFO com.affymetrix.main.OSGiHandler - loading sequenceViewer-10.0.0.jar 14:14:18.136 [main] INFO com.affymetrix.main.OSGiHandler - loading session-manager-10.0.0.jar 14:14:18.176 [main] INFO com.affymetrix.main.OSGiHandler - loading shared-lib-wrapper-10.0.0.jar 14:14:18.179 [main] INFO com.affymetrix.main.OSGiHandler - loading slf4j-api-1.7.36.jar 14:14:18.181 [main] INFO com.affymetrix.main.OSGiHandler - loading survey-10.0.0.jar 14:14:18.184 [main] INFO com.affymetrix.main.OSGiHandler - loading synonym-lookup-10.0.0.jar 14:14:18.186 [main] INFO com.affymetrix.main.OSGiHandler - loading thresholding-10.0.0.jar 14:14:18.188 [main] INFO com.affymetrix.main.OSGiHandler - loading track-operations-panel-10.0.0.jar 14:14:18.190 [main] INFO com.affymetrix.main.OSGiHandler - loading txw2-4.0.4.jar 14:14:18.192 [main] INFO com.affymetrix.main.OSGiHandler - loading update-10.0.0.jar 14:14:18.195 [main] INFO com.affymetrix.main.OSGiHandler - loading weblinks-10.0.0.jar 14:14:18.197 [main] INFO com.affymetrix.main.OSGiHandler - loading window-service-10.0.0.jar 14:14:18.199 [main] INFO com.affymetrix.main.OSGiHandler - loading xz-1.9.jar 14:14:18.199 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 14:14:18.199 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.xml.fastinfoset.FastInfoset 14:14:18.205 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 14:14:18.221 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 14:14:18.253 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 14:14:18.260 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: appstore 14:14:18.265 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bai 14:14:18.271 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 14:14:18.273 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 14:14:18.276 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 14:14:18.279 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 14:14:18.281 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig 14:14:18.282 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 14:14:18.358 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 14:14:18.361 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 14:14:18.362 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-codec 14:14:18.362 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-compress 14:14:18.362 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-csv 14:14:18.363 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-fileupload 14:14:18.364 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.commons-io 14:14:18.364 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 14:14:18.364 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 14:14:18.365 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 14:14:18.365 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 14:14:18.365 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-tab 14:14:18.367 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 14:14:18.368 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 14:14:18.370 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 14:14:18.370 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 14:14:18.372 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava.failureaccess 14:14:18.373 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 14:14:18.375 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 14:14:18.375 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 14:14:18.377 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.genotyping 14:14:18.379 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 14:14:18.380 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 14:14:18.382 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 14:14:18.383 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 14:14:18.383 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 14:14:18.383 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb 14:14:18.384 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 14:14:18.388 INFO com.affymetrix.igb.Activator - Verifying Jidesoft license 14:14:18.403 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 14:14:18.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 14:14:18.404 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 14:14:18.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 14:14:18.405 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 14:14:18.409 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 14:14:18.560 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 14:14:18.560 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.sun.istack.commons-runtime 14:14:18.560 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.activation-api 14:14:18.561 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: jakarta.xml.bind-api 14:14:18.561 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.core 14:14:18.561 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.jaxb.runtime 14:14:18.561 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate.jakarta 14:14:18.562 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 14:14:18.564 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 14:14:18.566 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 14:14:18.566 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 14:14:18.566 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 14:14:18.567 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 14:14:18.568 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 14:14:18.572 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 14:14:18.592 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 14:14:18.603 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.eventadmin 14:14:18.612 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 14:14:18.613 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 14:14:18.670 INFO org.eclipse.jetty.server.Server - jetty-11.0.18; built: 2023-10-27T02:14:36.036Z; git: 5a9a771a9fbcb9d36993630850f612581b78c13f; jvm 21.0.1+12-LTS 14:14:18.704 INFO o.e.j.s.s.DefaultSessionIdManager - Session workerName=node0 14:14:18.718 INFO o.e.j.server.handler.ContextHandler - Started o.e.j.s.ServletContextHandler@7fd69dd{/,null,AVAILABLE} 14:14:18.729 INFO org.eclipse.jetty.server.Server - Started Server@36b310aa{STARTING}[11.0.18,sto=0] @1833ms 14:14:18.790 INFO o.e.jetty.server.AbstractConnector - Started ServerConnector@5cb5bb88{HTTP/1.1, (http/1.1)}{localhost:7080} 14:14:18.790 INFO org.apache.felix.http - Started Jetty 11.0.18 at port(s) HTTP:7080 on context path / [minThreads=8,maxThreads=200,acceptors=2,selectors=8] 14:14:18.805 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 14:14:18.805 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 14:14:20.241 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.webconsole 14:14:20.278 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 14:14:20.282 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.component 14:14:20.283 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.log 14:14:20.283 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.function 14:14:20.283 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.util.promise 14:14:20.284 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.glassfish.hk2.osgi-resource-locator 14:14:20.293 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 14:14:20.298 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor 14:14:20.299 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 14:14:20.372 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 14:14:20.376 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 14:14:20.382 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 14:14:20.386 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 14:14:20.394 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 14:14:20.407 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 14:14:20.413 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 14:14:20.418 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 14:14:20.418 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 14:14:20.418 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 14:14:20.422 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 14:14:20.725 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/rnaseq/ 14:14:20.735 INFO o.lorainelab.igb.das.DasDataProvider - dasDsnUrl:https://genome.cse.ucsc.edu/cgi-bin/das/ 14:14:21.297 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/rnaseq/synonyms.txt 14:14:21.392 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/rnaseq/species.txt 14:14:21.711 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/quickload/ 14:14:21.762 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem 14:14:21.764 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem 14:14:21.765 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 14:14:21.769 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 14:14:21.773 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: null 14:14:21.774 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 14:14:21.776 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 14:14:21.793 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. 14:14:21.804 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. 14:14:21.804 INFO com.affymetrix.igb.Activator - Starting IGB 14:14:21.821 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 10.0.0 14:14:21.821 INFO com.affymetrix.igb.IGB - Java version: 21.0.1 from Azul Systems, Inc. 14:14:21.824 INFO com.affymetrix.igb.IGB - System memory: 4.3 GB 14:14:22.381 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/blueberry/ 14:14:22.572 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/blueberry/synonyms.txt 14:14:22.665 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/blueberry/species.txt 14:14:23.751 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/aloraine/.igb/bookmarks.html 14:14:23.753 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/aloraine/.igb/bookmarks.html~ 14:14:23.998 INFO c.a.igb.util.IGBTrustManager - Trusted Certificates:CN=genome.ucsc.edu,O=University of California\, Santa Cruz,ST=California,C=US; CN=AAA Certificate Services,O=Comodo CA Limited,L=Salford,ST=Greater Manchester,C=GB; CN=USERTrust RSA Certification Authority,O=The USERTRUST Network,L=Jersey City,ST=New Jersey,C=US; CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US 14:14:24.413 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 14:14:24.414 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 14:14:24.414 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 14:14:24.415 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@6aaa678d 14:14:24.415 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE thread set port failed due to (os/kern) invalid argument ./run_igb.sh: line 34: 91351 Trace/BPT trap: 5 java $JAVA_OPTS -jar igb_exe.jar
Scroll to the end to see where IGB crashed - repeated here for convenience:
... 14:14:24.413 INFO o.l.i.appstore.IgbAppServerLauncher - setPlugingManagerService START 14:14:24.414 INFO o.l.i.appstore.IgbAppServerLauncher - setPluginManagerService DONE 14:14:24.414 INFO o.l.i.appstore.IgbAppServerLauncher - activate START 14:14:24.415 INFO o.l.i.appstore.IgbAppServerLauncher - org.lorainelab.igb.plugin.manager.service.impl.PluginManagerServiceImpl@6aaa678d 14:14:24.415 INFO o.l.i.appstore.IgbAppServerLauncher - activate DONE thread set port failed due to (os/kern) invalid argument ./run_igb.sh: line 34: 91351 Trace/BPT trap: 5 java $JAVA_OPTS -jar igb_exe.jar
The above error occurred, and the "Problem report" window reporting the crash opened, with the following text:
Process: java [91351]
Path: /Users/USER/*/java
Identifier: com.azul.zulu.java
Version: 21.0.1 (12)
Code Type: X86-64 (Native)
Parent Process: ??? [91350]
Responsible: Terminal [470]
User ID: 501Date/Time: 2024-01-09 14:14:24.701 -0600
OS Version: macOS 11.7.10 (20G1427)
Report Version: 12
Bridge OS Version: 7.6 (20P6072)
Anonymous UUID: EFD07912-3C36-78DF-2007-79B53BCB2FF4Sleep/Wake UUID: 6AA0B45E-8219-4EAF-B0DB-33BB4BC5AAEE
Time Awake Since Boot: 460000 seconds
Time Since Wake: 1000 secondsSystem Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFYTermination Signal: Trace/BPT trap: 5
Termination Reason: Namespace SIGNAL, Code 0x5
Terminating Process: exc handler [91351]Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libjfxwebkit.dylib 0x00000001f5f98f01 0x1f32d9000 + 46923521
1 libjfxwebkit.dylib 0x00000001f5d9c07c 0x1f32d9000 + 44839036
2 libjfxwebkit.dylib 0x00000001f5c4a434 0x1f32d9000 + 43455540
3 libjfxwebkit.dylib 0x00000001f5649d61 0x1f32d9000 + 37162337
4 libjfxwebkit.dylib 0x00000001f5959883 0x1f32d9000 + 40372355
5 libjfxwebkit.dylib 0x00000001f5022f46 JSEvaluateScript + 806
6 libjfxwebkit.dylib 0x00000001f40268c7 0x1f32d9000 + 13949127
7 libjfxwebkit.dylib 0x00000001f33a7386 Java_com_sun_webkit_WebPage_twkExecuteScript + 86
8 ??? 0x000000012101b980 0 + 4848728448
9 ??? 0x0000000121017166 0 + 4848709990
Nowlan Freese - please see above error report.
It looks like there is something going wrong with the App Manager code.
There seems to be a bug with "web kit" (not sure what this is) in Apple OS 11 (Big Sur), according to this OpenJDK "bugs" post: https://bugs.openjdk.org/browse/JDK-8320267
quoting:
Starting JavaFX 21.0.1, on macOS 11 (Intel), when the WebView loads any URL it crashes.
It works fine with JavaFX 21, or on macOS 12, 13, 14.
This means that it is related to the update to WebKit 616.1.
To reproduce, run the attached test with JDK 17 or greater.
I checked to see if I could run main-JDK21, downloaded and installed from IGB team repository Downloads section at https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-macos-universal-main-JDK21-with-javafx-no-theme.dmg.
This version also crashed:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libjfxwebkit.dylib 0x00000000a8072f01 0xa53b3000 + 46923521 1 libjfxwebkit.dylib 0x00000000a7e7607c 0xa53b3000 + 44839036 2 libjfxwebkit.dylib 0x00000000a7d24434 0xa53b3000 + 43455540 3 libjfxwebkit.dylib 0x00000000a7723d61 0xa53b3000 + 37162337 4 libjfxwebkit.dylib 0x00000000a7a33883 0xa53b3000 + 40372355 5 libjfxwebkit.dylib 0x00000000a70fcf46 JSEvaluateScript + 806 6 libjfxwebkit.dylib 0x00000000a61008c7 0xa53b3000 + 13949127 7 libjfxwebkit.dylib 0x00000000a5481386 Java_com_sun_webkit_WebPage_twkExecuteScript + 86 8 ??? 0x000000001f837980 0 + 528710016 9 ??? 0x000000001f833166 0 + 528691558 10 ??? 0x000000001f833166 0 + 528691558 11 ??? 0x000000001f833166 0 + 528691558 12 ??? 0x000000001f833362 0 + 528692066 13 ??? 0x000000001f8337ee 0 + 528693230 14 ??? 0x000000001f833166 0 + 528691558 15 ??? 0x0000000018f5987c 0 + 418748540 16 ??? 0x000000001f833362 0 + 528692066 17 ??? 0x000000001f8337ee 0 + 528693230 18 ??? 0x000000001f82bcc6 0 + 528661702 19 libjvm.dylib 0x000000000886b7b4 JavaCalls::call_helper(JavaValue*, methodHandle const&, JavaCallArguments*, JavaThread*) + 692 20 libjvm.dylib 0x00000000088d6eef jni_invoke_nonstatic(JNIEnv_*, JavaValue*, _jobject*, JNICallType, _jmethodID*, JNI_ArgumentPusher*, JavaThread*) + 847 21 libjvm.dylib 0x00000000088dbe43 jni_CallVoidMethod + 403 22 libglass.dylib 0x0000000031a90131 0x31a8a000 + 24881 23 com.apple.Foundation 0x00007fff2149ebb1 __NSThreadPerformPerform + 204 24 com.apple.CoreFoundation 0x00007fff206edcdc __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 25 com.apple.CoreFoundation 0x00007fff206edc44 __CFRunLoopDoSource0 + 180 26 com.apple.CoreFoundation 0x00007fff206eda26 __CFRunLoopDoSources0 + 340 27 com.apple.CoreFoundation 0x00007fff206ec3ec __CFRunLoopRun + 893 28 com.apple.CoreFoundation 0x00007fff206eb9ac CFRunLoopRunSpecific + 563 29 com.apple.HIToolbox 0x00007fff289361f3 RunCurrentEventLoopInMode + 292 30 com.apple.HIToolbox 0x00007fff28935f55 ReceiveNextEventCommon + 587 31 com.apple.HIToolbox 0x00007fff28935cf3 _BlockUntilNextEventMatchingListInModeWithFilter + 70 32 com.apple.AppKit 0x00007fff22ef5ad2 _DPSNextEvent + 864 33 com.apple.AppKit 0x00007fff22ef42a5 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364 34 libosxapp.dylib 0x000000000e9b95aa -[NSApplicationAWT nextEventMatchingMask:untilDate:inMode:dequeue:] + 122 35 com.apple.AppKit 0x00007fff22ee65c9 -[NSApplication run] + 586 36 libosxapp.dylib 0x000000000e9b9379 +[NSApplicationAWT runAWTLoopWithApp:] + 169 37 libsplashscreen.dylib 0x000000000e99a809 __SplashInitPlatform_block_invoke + 73 38 libosxapp.dylib 0x000000000e9bb04f +[ThreadUtilities invokeBlockCopy:] + 15 39 com.apple.Foundation 0x00007fff2149ebb1 __NSThreadPerformPerform + 204 40 com.apple.CoreFoundation 0x00007fff206edcdc __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 41 com.apple.CoreFoundation 0x00007fff206edc44 __CFRunLoopDoSource0 + 180 42 com.apple.CoreFoundation 0x00007fff206ed9c4 __CFRunLoopDoSources0 + 242 43 com.apple.CoreFoundation 0x00007fff206ec3ec __CFRunLoopRun + 893 44 com.apple.CoreFoundation 0x00007fff206eb9ac CFRunLoopRunSpecific + 563 45 libjli.dylib 0x00000000082a3ee2 CreateExecutionEnvironment + 386 46 libjli.dylib 0x000000000829f8bd JLI_Launch + 1357 47 com.install4j.1717-8724-7098-6386.22 0x00000000062d68e1 -[Launcher launch] + 2257 48 com.install4j.1717-8724-7098-6386.22 0x00000000062d7001 launcher_main + 625 49 com.install4j.1717-8724-7098-6386.22 0x00000000062d7172 main + 34 50 libdyld.dylib 0x00007fff20610f3d start + 1
Suggestion: Use install4J interface to build an installer that has JavaFX 20.0.0 instead of JavaFX 20.0.1. Test it on the Big Sur computer.
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
Following up on suggestion from Nowlan Freese (Nowlan Freese) I downloaded and set up the next-to-last release of the Azul build of JDK 21, which has JavaFX 20.0.0 instead of JavaFX 20.0.1:
local aloraine$ pwd /Users/aloraine/JDKs/zulu21.28.85-ca-fx-jdk21.0.0-macosx_x64
Confirming the JavaFX version:
local aloraine$ cat lib/javafx.properties javafx.version=21.0.0 javafx.runtime.version=21.0.0+102 javafx.runtime.build=102
Setting this new build to be my system's java by adding the following line to my ~/.bash_profile file:
export JAVA_HOME="/Users/aloraine/JDKs/zulu21.28.85-ca-fx-jdk21.0.0-macosx_x64"
Built this version of IGB 10.0.0:
local aloraine$ git status On branch main-JDK21-with-javafx-no-theme ... local aloraine$ git ls 3ebd3651f5 (HEAD -> main-JDK21-with-javafx-no-theme, origin/main-JDK21-with-javafx-no-theme) rolling back temporary change
Ran IGB with:
aloraine$ ./run_igb.sh
The result: IGB window opened as expected.
Now, checking to see if changing the JAVA_HOME back to the latest Azul JDK 21 release causes the observed bug to re-occur.
Changed JAVA_HOME back to latest Azul JDK 21 release:
export JAVA_HOME="/Users/aloraine/JDKs/zulu21.30.15-ca-fx-jdk21.0.1-macosx_x64"
Confirming that this JDK 21 release does indeed contain JavaFX version 21.0.1 and not version 21.0.0:
local aloraine$ pwd /Users/aloraine/JDKs/zulu21.30.15-ca-fx-jdk21.0.1-macosx_x64 local aloraine$ cat lib/javafx.properties javafx.version=21.0.1 javafx.runtime.version=21.0.1+101 javafx.runtime.build=101
Re-building IGB with:
local aloraine$ mvn clean install
Tested whether IGB can run with:
local aloraine$ ./run_igb.sh
The result:
IGB cannot run on my system using this newer JDK build from Azul.
Conclusion:
My MacOS version 11.7.10 (20G1427) Intel computer cannot run IGB using Azul JDK21 build zulu8.62.0.19-ca-fx-jdk8.0.332-macosx_x64. However, my computer can run IGB using Azul JDK21 build /zulu21.28.85-ca-fx-jdk21.0.0-macosx_x64.
Therefore, I recommend that we create some new installers that use the older Azul build for the MacOS platform and confirm that these can run fine on Intel and ARM machines. If it can run fine on the different OS's likely to be present on users' computers, we should use this slightly older build. Also, we should be diligent at checking future Azul releases in case newer ones correct the error.
I do not think we need to downgrade the Windows and Linux installers, however.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
2022 MacBook Air M2 - 14.2.1
2021 MacBook Pro M1 Pro - 12.4
2020 MacBook Air M1 - 13.5.2
2019 MacBook Pro Intel - 11.7.10
2017 MacBook Pro Intel - 13.6.3
2015 MacBook Pro Intel - 12.6
I checked on the 2020 MacBook Pro running MacOS 11.6.2 and the 21.0.1 JDK did crash as Dr. Loraine had reported on her machine.
Before rebuilding JRE bundle, let's test the App Store functionality on the Big Sur Intel machine.
Testing the macos-universal-21.0.0.tar.gz found in the jre-bundles-install4j repo by using it to create an installer from the main-JDK21-with-javafx-no-theme branch, and then test that installer on the following machines:
2022 MacBook Air M2 - 14.2.1 -> Successful install/run IGB/App Manager/App Store
2022 MacBook Air M2 - 13.5.2 -> Successful install/run IGB/App Manager/App Store
2020 MacBook Air M1 - 13.5.2 -> Successful install/run IGB/App Manager/App Store
2019 MacBook Pro Intel - 11.7.10 -> Successful install/run IGB/App Manager/App Store
2019 MacBook Pro Intel - 11.6.2 -> Successful install/run IGB/App Manager/App Store
2017 MacBook Pro Intel - 13.6.3 -> Successful install/run IGB/App Manager/App Store
JDK 21.0.1 release notes. I don't see anything critical in the 21.0.1 release notes, and the 21.0.0 JRE is working across intel/M and on the various macOS versions above. I think we move forward with the 20.0.0 JRE for Mac.
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Summary of new work:
- Ann ran Install4J using instructions from Nowlan.
- Selected Azul Zulu build version 21.0.0 (see attached image from Install4J interface)
- Created a bundle JRE for MacOS and uploaded it to https://bitbucket.org/lorainelab/jre-bundles-install4j/downloads/ using Install4J file, keeping the file name of macos-universal-21.0.0.tar.gz
- On my local, unpacked macos-universal-21.0.0.tar.gz (becomes "Contents" directory) and inspected unpacked contents as follows
local aloraine$ pwd /Users/aloraine/Downloads/Contents local aloraine$ ls Home Info.plist MacOS local aloraine$ cat Home/lib/javafx.properties javafx.version=21.0.0 javafx.runtime.version=21.0.0+102 javafx.runtime.build=102
Confirmed java version with:
local aloraine$ pwd
/Users/aloraine/Downloads/Contents/Home/bin
local aloraine$ ./java --version
openjdk 21 2023-09-19
OpenJDK Runtime Environment Zulu21.28+85-CA (build 21+35)
OpenJDK 64-Bit Server VM Zulu21.28+85-CA (build 21+35, mixed mode)
| Attachment | macosjdk.png [ 18174 ] |
Edited Dockerfile and used it to build a new image with:
docker build -t igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 .
Cloned target branch:
git clone --single-branch --branch main-JDK21-with-javafx-no-theme https://bitbucket.org/lorainelab/integrated-genome-browser build
Running Docker image interactive session with:
docker run -i -t -v ~/build:/build --env-file env_vars --workdir /build igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 /bin/bash
Inside container, built installers with:
mvn install -P release-bitbucket-pipelines
Installer for MacOS build failed with:
[INFO] Creating media file 'Mac_OS X_universal':
[INFO] install4j: compilation failed. Reason: java.io.FileNotFoundException: Could not find JRE bundle file /root/.local/share/install4j/v10/jres/macos-universal-21.0.1.tar.gz
To fix this error, need to modify the install4J configuration file.
Making a new branch to do this and repeating the above steps.
Made branch IGBF-3508 on my fork https://bitbucket.org/aloraine/integrated-genome-browser to fix the above-mentioned error.
Cloned my new branch onto the docker host (as ec2-user) with
git clone --single-branch --branch IGBF-3508 https://bitbucket.org/aloraine/integrated-genome-browser build
As ec2-user, started interactive docker container session with:
docker run -i -t -v ~/build:/build --env-file env_vars --workdir /build igb-maven-install4j:I4J10-jre-21.0.1-21.0.0 /bin/bash
Inside container, attempted built installers with:
mvn install -P release-bitbucket-pipelines
Downloaded MacOS installer to my computer and ran it. Observed that IGB started.
Because the Docker image was able to build a working MacOS installer, re-tagged the new image with:
docker.bioviz.org ec2-user $ docker tag f0a8b3d62078 lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0
Confirmed the tag with:
docker.bioviz.org ec2-user $ docker image ls REPOSITORY TAG IMAGE ID CREATED SIZE lorainelab/igb-maven-install4j I4J10-jre-21.0.1-21.0.0 f0a8b3d62078 15 minutes ago 2.86GB igb-maven-install4j I4J10-jre-21.0.1-21.0.0 f0a8b3d62078 15 minutes ago 2.86GB <none> <none> 4e0fb64a282f 19 hours ago 2.86GB igb-maven-install4j I4J10-jre-21.0.1 91f23d890b25 4 weeks ago 2.86GB igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 5 weeks ago 4.12GB lorainelab/igb-maven-install4j I4J10-nonuniversal-full-jre-21.0.1 2e7cb3f63270 5 weeks ago 4.12GB
Logged into our docker hub account with:
docker login -u aloraine
Pushed new image with:
docker push lorainelab/igb-maven-install4j:I4J10-jre-21.0.1-21.0.0
Confirmed that the image is properly uploaded by seeing it listed here: https://hub.docker.com/r/lorainelab/igb-maven-install4j/tags
Updated bitbucket pipeline configuration file to use the new image. Committed the change to my branch IGBF-3508 and pushed to fork.
The push triggered pipelines to build the new installers. Installers are available in the fork's Downloads section here: https://bitbucket.org/aloraine/integrated-genome-browser/downloads/
Downloaded MacOS installer and confirmed it could run on my Big Sur Intel MacOS computer.
Submitted PR from my fork and branch to target branch main-JDK21-with-javafx-no-theme on the team repository.
Merged the PR with the target branch main-JDK21-with-javafx-no-theme.
Launched pipeline to build branch installers as usual.
Installers are built and ready for testing.
See:
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-macos-universal-main-JDK21-with-javafx-no-theme.dmg
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-windows-main-JDK21-with-javafx-no-theme_amd64.exe
- https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-linux-main-JDK21-with-javafx-no-theme_amd64.sh
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
Note: Also, updating dockerfile and pushing to repository lorainelab/integrated-genome-browser-docker.git.
Tested installer and IGB on MacOS 13.6.3 and Windows 10 - both worked successfully.
The installer worked on MacOS 14.2.1. I also tested the installer on Windows 11 which seemed to work, though I did not get a chance to open IGB and check its functionality before my laptop died.
Pushed new Dockerfile to https://bitbucket.org/lorainelab/integrated-genome-browser-docke branch jdk21.
Moving to DONE because all the code has been tested and all is fine.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] |
We were seeing an error when running the pipeline where libfontmanager.so is missing from Install4Jv10's own JRE (downloaded the Install4Jv10 debian distribution). Install4J is using a version of JDK17 that is missing libfontmanager.so. David removed their JRE and added a different JRE 17 for Install4J to use (you can see this in the Docker file). So this is why there are two JREs being installed onto the Docker Image. We also had to install a fontmanager/config on the Docker image for Install4J to work correctly.