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biocodellc / biocode-lims

The Biocode LIMS plugin integrates Geneious with your lab workflow, allowing you to track processes through tissue sample, extraction, PCR, sequencing and assembly. It is best suited for large scale DNA barcoding efforts.
https://github.com/biocodellc/biocode-lims/wiki
BSD 3-Clause "New" or "Revised" License
9 stars 0 forks source link

Biocode Plugin 2.8.12: RuntimeException in GDialog.pack() (group 10918) #9

Open jdeck88 opened 9 years ago

jdeck88 commented 9 years ago

This is https://bugs.openjdk.java.net/browse/JDK-7124363 but for the life of me I can't figure out if they've ported it to JDK8. I guess not since it's failing for us

It sounds like the workaround is to make sure we're never trying to pop up a dialog over a FileDialog.

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.0.2
OS: Mac OS 10.10.5 (x86_64)
Java Version: 1.8.0_60 (64 bit)
Application Build Date: 2009-07-02 14:32
User name: matthew
Email: matthew@biomatters.com
Message: WTF... what happened here? JDK bug? Bug caused by my memory leak fix? Something else?
Memory Usage: 284 / 4092 / 16384 MB [After previous GC: heap total:261/4092 Par Eden Space:0/32 Par Survivor Space:3/4 CMS Old Gen:258/4056]
Data on Network: false
Data Directory: /Users/matthew/Geneious 9.0 Data
Stack Analysis: Biocode Plugin 2.8.12
Thread: Thread[Thread-40,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=54338

[MBP-742] created by talkback

jdeck88 commented 9 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.0.2
OS: Mac OS 10.11 (x86_64)
Java Version: 1.8.0_60 (64 bit)
Application Build Date: 2015-10-06 17:24
User name: Eldin
Memory Usage: 482 / 7996 / 16384 MB [After previous GC: heap total:333/7996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:329/7960]
Data on Network: false
Data Directory: /Users/Eldin/GeneiousDBs/MainDB
Stack Analysis: Biocode Plugin 2.8.11
Thread: Thread[Thread-21,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=54714

by talkback

jdeck88 commented 9 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.0.2
OS: Mac OS 10.11 (x86_64)
Java Version: 1.8.0_60 (64 bit)
Application Build Date: 2015-10-06 17:24
User name: Eldin
Memory Usage: 437 / 7996 / 16384 MB [After previous GC: heap total:315/7996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:311/7960]
Data on Network: false
Data Directory: /Users/Eldin/GeneiousDBs/MainDB
Stack Analysis: Biocode Plugin 2.8.11
Thread: Thread[Thread-42,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=54716

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.0.5
OS: Mac OS 10.11.2 (x86_64)
Java Version: 1.8.0_60 (64 bit)
Application Build Date: 2015-12-10 09:23
User name: brunosimoes
Memory Usage: 65 / 9996 / 32768 MB [After previous GC: heap total:50/9996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:46/9960]
Data on Network: false
Data Directory: /Users/brunosimoes/Documents/Geneious_AGL
Stack Analysis: Biocode Plugin 2.8.11
Thread: Thread[Thread-40,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=57167

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.0.5
OS: Mac OS 10.10.5 (x86_64)
Java Version: 1.8.0_60 (64 bit)
Application Build Date: 2015-12-10 09:23
User name: CarolinePL
Memory Usage: 191 / 3996 / 8192 MB [After previous GC: heap total:183/3996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:179/3960]
Data on Network: false
Data Directory: /Users/CarolinePL/Geneious 9.0 Data
Stack Analysis: Biocode Plugin 2.8.11
Thread: Thread[Thread-818,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=58303

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.2
OS: Mac OS 10.10.5 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-02-29 17:18
User name: CarolinePL
Memory Usage: 324 / 3996 / 8192 MB [After previous GC: heap total:191/3996 Par Eden Space:0/32 Par Survivor Space:2/4 CMS Old Gen:188/3960]
Data on Network: false
Data Directory: /Users/CarolinePL/Geneious9.1Data
Stack Analysis: Biocode Plugin 2.8.11
Thread: Thread[Thread-165,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,GenBank Submission,Mafft Multiple Alignment,PAUP* Plugin,FastTree,Garli,MrBayes Plugin,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=59106

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.2
OS: Windows 7 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-02-29 17:18
User name: LeeSangHyeob
Memory Usage: 10815 / 14332 / 16340 MB [After previous GC: heap total:10583/14332 Par Eden Space:0/32 Par Survivor Space:3/4 CMS Old Gen:10579/14296]
Data on Network: true
Data Directory: \\223.195.77.150\Cucumber\Geneious 9.1 Data
Stack Analysis: Sequence View 9.1.2
Thread: Thread[ask user if they wish to force quit every 10 seconds,6,main]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: BBDuk Trimmer,BBMap,Bowtie short read mapper,Cap3 Assembly,Sequence Classifier,Coiled coils prediction,Complement or Reverse Only,CpG Islands,EuPathDB Plugin,GenBank Submission,Glimmer Gene Prediction,LASTZ alignment,Mafft Multiple Alignment,Microsatellite Plugin,MIRA de novo assembler,EMBOSS Mutate and Shuffle,EMBOSS Nucleotide Analysis,Collaboration,PAUP* Plugin,Phobos Tandem Repeat Finder,EMBOSS Protein Analysis,Repeat Finder,PDB Structure Aligner,Velvet Assembly,InterProScan,FastTree,PHYML,FreeBayes_Variant_Finder,Garli,Mauve Plugin,DualBrothers Recombination Detection,MrBayes Plugin,Transmembrane Prediction Tool,RAxML,Contig Sorter,Heterozygote Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=59317

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.5
OS: Mac OS 10.11.5 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-06-11 21:21
User name: barcode
Memory Usage: 149 / 2996 / 8192 MB [After previous GC: heap total:46/2996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:42/2960]
Data on Network: false
Data Directory: /Users/barcode/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.0
Thread: Thread[Thread-21,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: BBDuk Trimmer,BBMap,Biocode Plugin,Bowtie short read mapper,Mafft Multiple Alignment,FastTree,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=62564

by talkback

jdeck88 commented 8 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.5
OS: Windows 8.1 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-06-11 21:21
User name: mgh
Memory Usage: 622 / 6094 / 8097 MB [After previous GC: heap total:482/6094 Par Eden Space:0/32 Par Survivor Space:0/4 CMS Old Gen:482/6058]
Data on Network: false
Data Directory: C:\Users\mgh\Geneious 9.1 Data (exists=true)
Application Directory: C:\Program Files\Geneious (exists=true)
Thread: Thread[AWT-EventQueue-0,6,main]
Exception Message: couldn't create component peer
Installed plugin list: Collaboration
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=62862

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.4
OS: Mac OS 10.11.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-05-09 16:27
User name: lopezi
Message:

Memory Usage: 115 / 3996 / 8192 MB [After previous GC: heap total:98/3996 Par Eden Space:0/32 Par Survivor Space:0/4 CMS Old Gen:98/3960]
Data on Network: false
Data Directory: /Users/lopezi/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.1
Thread: Thread[Thread-26,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Sequence Classifier,Mafft Multiple Alignment,PAUP* Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=64969

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.6
OS: Mac OS 10.11.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-09-19 13:04
User name: lopezi
Memory Usage: 121 / 1996 / 8192 MB [After previous GC: heap total:96/1996 Par Eden Space:0/32 Par Survivor Space:0/4 CMS Old Gen:96/1960]
Data on Network: false
Data Directory: /Users/lopezi/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.1
Thread: Thread[Thread-26,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Sequence Classifier,GenBank Submission,Mafft Multiple Alignment,PAUP* Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=65255

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.5
OS: Windows 7 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-06-11 21:21
User name: bu002
Message: fengjiao.bu@wur.nl
Memory Usage: 1882 / 6062 / 8066 MB [After previous GC: heap total:1052/6062 Par Eden Space:0/32 Par Survivor Space:1/4 CMS Old Gen:1050/6026]
Data on Network: false
Data Directory: D:\D drive\Geneious R9 Data Storage (exists=true)
Application Directory: D:\D drive\Geneious R9 20160902 (exists=true)
Stack Analysis: Sequence View 9.1.5
Thread: Thread[AWT-EventQueue-0,6,main]
Exception Message: couldn't create component peer
Installed plugin list: Mafft Multiple Alignment,FastTree
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=65572

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.2
OS: Mac OS 10.11.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-02-29 17:18
User name: cran5048
Message: Loading a spreadsheet into the FIMS field
Memory Usage: 76 / 996 / 16384 MB [After previous GC: heap total:58/996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:54/960]
Data on Network: false
Data Directory: /Users/cran5048/Geneious 9.1 Data
Stack Analysis: Biocode Plugin 3.0.1
Thread: Thread[Thread-18,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: PAUP* Plugin,Biocode Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=65883

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.6
OS: Mac OS 10.10.5 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-09-19 13:04
User name: Sabrina
Memory Usage: 270 / 996 / 16384 MB [After previous GC: heap total:182/996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:178/960]
Data on Network: false
Data Directory: /Users/Sabrina/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.1
Thread: Thread[Thread-57,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=66068

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.5
OS: Windows 7 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-06-11 21:21
User name: LZH
Memory Usage: 2446 / 30702 / 32710 MB [After previous GC: heap total:1313/30702 Par Eden Space:0/32 Par Survivor Space:3/4 CMS Old Gen:1310/30666]
Data on Network: false
Data Directory: G:\Geneious 9.1 Data (exists=true)
Application Directory: D:\Program Files\Geneious\Geneious (exists=true)
Thread: Thread[AWT-EventQueue-0,6,main]
Exception Message: couldn't create component peer
Installed plugin list: CpG Islands,GenBank Submission,Mafft Multiple Alignment,MIRA de novo assembler,EMBOSS Nucleotide Analysis,PAUP* Plugin,Phobos Tandem Repeat Finder,EMBOSS Protein Analysis,Repeat Finder,Velvet Assembly,FastTree,PHYML,Mauve Plugin,DualBrothers Recombination Detection,MrBayes Plugin,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=70019

by talkback

jdeck88 commented 7 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.8
OS: Mac OS 10.12.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2017-02-14 11:06
User name: amanda.windsor
Memory Usage: 156 / 9996 / 16384 MB [After previous GC: heap total:111/9996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:107/9960]
Data on Network: false
Data Directory: /Users/amanda.windsor/Geneious Data Restored (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.1
Thread: Thread[Thread-18,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Document Field Remover,Mafft Multiple Alignment
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=71624

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.8
OS: Mac OS 10.12.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2017-02-14 11:06
User name: amanda.windsor
Memory Usage: 134 / 9996 / 16384 MB [After previous GC: heap total:112/9996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:108/9960]
Data on Network: false
Data Directory: /Users/amanda.windsor/Geneious Data Restored (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.4
Thread: Thread[Thread-19,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Document Field Remover,GenBank Submission,Mafft Multiple Alignment,FastTree,PHYML,Garli,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=74851

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.7
OS: Mac OS 10.12.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-11-22 10:49
User name: jessicabudke
Memory Usage: 254 / 13996 / 16384 MB [After previous GC: heap total:114/13996 Par Eden Space:0/32 Par Survivor Space:3/4 CMS Old Gen:110/13960]
Data on Network: false
Data Directory: /Users/jessicabudke/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.4
Thread: Thread[Thread-48,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Complement or Reverse Only,PAUP* Plugin,Garli,MrBayes Plugin,RAxML,Biocode Plugin
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=76287

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: Current
Geneious Version: 9.1.8
OS: Mac OS 10.12.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2017-02-14 11:06
User name: jessicabudke
Memory Usage: 172 / 13996 / 16384 MB [After previous GC: heap total:53/13996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:49/13960]
Data on Network: false
Data Directory: /Users/jessicabudke/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious 2.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.4
Thread: Thread[Thread-17,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Complement or Reverse Only,PAUP* Plugin,Garli,MrBayes Plugin,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=76289

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: EarlierDuringThisRunOfGeneious
Geneious Version: 9.1.8
OS: Mac OS 10.12.6 (x86_64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2017-02-14 11:06
User name: jessicabudke
Memory Usage: 112 / 13996 / 16384 MB [After previous GC: heap total:42/13996 Par Eden Space:0/32 Par Survivor Space:4/4 CMS Old Gen:38/13960]
Data on Network: false
Data Directory: /Users/jessicabudke/Geneious 9.1 Data (exists=true)
Application Directory: /Applications/Geneious 2.app/Contents/Java (exists=true)
Stack Analysis: Biocode Plugin 3.0.4
Thread: Thread[Thread-17,6,]
Exception Message: java.lang.reflect.InvocationTargetException
Installed plugin list: Biocode Plugin,Complement or Reverse Only,PAUP* Plugin,Garli,MrBayes Plugin,RAxML
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=76290

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.8
OS: Windows 7 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2017-02-14 11:06
User name: elm280
Memory Usage: 152 / 6078 / 8082 MB [After previous GC: heap total:73/6078 Par Eden Space:0/32 Par Survivor Space:0/4 CMS Old Gen:72/6042]
Data on Network: false
Data Directory: C:\Users\elm280\Documents\Geneious restore data 10.18.17 (exists=true)
Application Directory: C:\Program Files\Geneious (exists=true)
Thread: Thread[AWT-EventQueue-0,6,main]
Exception Message: couldn't create component peer
Installed plugin list: Collaboration,PDB Structure Aligner,Transmembrane Prediction Tool
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=76748

by talkback

jdeck88 commented 6 years ago

Incident Sequence: 1
Incident Age: DuringAPreviousRunOfGeneious
Geneious Version: 9.1.7
OS: Windows 10 (amd64)
Java Version: 1.8.0_71 (64 bit)
Application Build Date: 2016-11-22 10:49
User name: Ashleigh.deKlerk
Email: ashleigh.deklerk@nhls.ac.za
Memory Usage: 524 / 2990 / 3992 MB [After previous GC: heap total:342/2990 Par Eden Space:0/32 Par Survivor Space:0/4 CMS Old Gen:341/2954]
Data on Network: false
Data Directory: C:\Users\ashleigh.deklerk\Geneious Data Restored (exists=true)
Application Directory: C:\Program Files\Geneious (exists=true)
Thread: Thread[AWT-EventQueue-0,6,main]
Exception Message: couldn't create component peer
Installed plugin list:
Full Details: http://bios.biomatters.com/viewTalkbackIncident.htm?id=80362

by talkback

jdeck88 commented 6 years ago

Is duplicated by: GH-755