[IGBF-3126] Investigate Monterrey upgrade problem - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Blocker
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.10 Major Release
Labels:
None

Story Points:
1
Epic Link:
Improve IGB for users
Sprint:
Summer 1 2022 May 23

Description

Report from user:

Dear Ann,

I recently upgraded my MacOS from El Capitan (10.11) to Monterey (12) and IGB stopped working. I have been using IGB for many years before that without major issues.

Attached is a text file with the system info, and the error log.

In most cases, IGB already crashes before opening (‘quit unexpectedly”), sometimes it opens ok at first, but then crashes as soon as I try to load data files.

Any help would be appreciated.

(I submitted the same crash report using the feedback form, but am not sure whether it got through as I don’t have a JIRA account.)

Thanks.

Paul Labhart

Attachments

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Attachments

hs_err_pid5885.log
64 kB
24/May/22 10:35 AM
IGB crash info.txt
1 kB
24/May/22 10:35 AM

Issue Links

relates to

IGBF-3104 Investigate IGB crash on MacOS

Closed

IGBF-3123 Remove feedback form from BioViz.org

Closed

Activity

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Ann Loraine created issue - 24/May/22 10:33 AM

Ann Loraine made changes - 24/May/22 10:33 AM

Field	Original Value	New Value
Epic Link		IGBF-1765 [ 17855 ]

Ann Loraine made changes - 24/May/22 10:33 AM

Link

This issue relates to ~~IGBF-3123~~ [ ~~IGBF-3123~~ ]

Ann Loraine made changes - 24/May/22 10:33 AM

Link

This issue relates to ~~IGBF-3104~~ [ ~~IGBF-3104~~ ]

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Ann Loraine added a comment - 24/May/22 10:34 AM - edited

Loraine reply:

Hello,

Thank you very much for the report. This is very helpful!

We've seen similar errors with a few other IGB users.

Can you try this?

Uninstall the version of IGB that is on your computer currently

Please download and run this new IGB installer to install IGB 9.1.8 - https://bitbucket.org/aloraine/integrated-genome-browser/downloads/Zulu-IGB-macos-9.1.8.dmg

This new installer includes IGB 9.1.8 and a version of java that I believe will be compatible with your computer.

If you do this, could let me know how it goes?

Warm regards and thank you for using IGB,

Ann

and later:

Thanks also for letting me know about the broken feedback form. I appreciate it!

Show

Ann Loraine added a comment - 24/May/22 10:34 AM - edited Loraine reply: Hello, Thank you very much for the report. This is very helpful! We've seen similar errors with a few other IGB users. Can you try this? Uninstall the version of IGB that is on your computer currently Please download and run this new IGB installer to install IGB 9.1.8 - https://bitbucket.org/aloraine/integrated-genome-browser/downloads/Zulu-IGB-macos-9.1.8.dmg This new installer includes IGB 9.1.8 and a version of java that I believe will be compatible with your computer. If you do this, could let me know how it goes? Warm regards and thank you for using IGB, Ann and later: Thanks also for letting me know about the broken feedback form. I appreciate it!

Ann Loraine made changes - 24/May/22 10:35 AM

Attachment

hs_err_pid5885.log [ 17235 ]

Ann Loraine made changes - 24/May/22 10:35 AM

Attachment

IGB crash info.txt [ 17236 ]

Ann Loraine made changes - 24/May/22 10:35 AM

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Ann Loraine added a comment - 24/May/22 10:40 AM

From the IGB crash info report:

The crash happened outside the Java Virtual Machine in native code.

I think IGB uses some native MacOS code to display MacOS native file choosers. This might be the culprit.

Show

Ann Loraine added a comment - 24/May/22 10:40 AM From the IGB crash info report: The crash happened outside the Java Virtual Machine in native code. I think IGB uses some native MacOS code to display MacOS native file choosers. This might be the culprit.

Ann Loraine made changes - 24/May/22 10:42 AM

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Ann Loraine added a comment - 24/May/22 4:56 PM

Reply from user:

Hi Ann,

I installed the Zulu-IGB-macos-9.1.8 and it seems to work great!

This really appears to have fixed the issue, and I hope it will hold up upon further testing.

Thank you very much.

(Regarding the JIRA submission: I don’t think there is any confidential information in my submitted documents. Thanks for the alert though.)

Paul

Show

Ann Loraine added a comment - 24/May/22 4:56 PM Reply from user: Hi Ann, I installed the Zulu-IGB-macos-9.1.8 and it seems to work great! This really appears to have fixed the issue, and I hope it will hold up upon further testing. Thank you very much. (Regarding the JIRA submission: I don’t think there is any confidential information in my submitted documents. Thanks for the alert though.) Paul

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Ann Loraine added a comment - 24/May/22 4:56 PM - edited

Problem solved. Moving to Needs First Level Review for Nowlan Freese or Karthik Raveendran to take a look.

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Ann Loraine added a comment - 24/May/22 4:56 PM - edited Problem solved. Moving to Needs First Level Review for Nowlan Freese or Karthik Raveendran to take a look.

Ann Loraine made changes - 24/May/22 4:56 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 24/May/22 4:57 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

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Nowlan Freese added a comment - 02/Jun/22 10:24 AM

Reply from user who tried out zulu install on Mac:

As of today, the IGB of the new version did not crash anymore.

I guess it might continue to be OK. Just let you know this and thank you for your help.

Best regards,
Lingrui

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Nowlan Freese added a comment - 02/Jun/22 10:24 AM Reply from user who tried out zulu install on Mac: As of today, the IGB of the new version did not crash anymore. I guess it might continue to be OK. Just let you know this and thank you for your help. Best regards, Lingrui