simple 20-Nov-2024 00:00:00 Build Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29) started building on agent Default Agent simple 20-Nov-2024 00:00:00 simple 20-Nov-2024 00:00:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 simple 20-Nov-2024 00:00:00 Executing build Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29) simple 20-Nov-2024 00:00:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 20-Nov-2024 00:00:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 simple 20-Nov-2024 00:00:00 Updating source code to revision: 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9 simple 20-Nov-2024 00:00:00 Fetching 'refs/heads/releases/Release_2_11_4_Branch' from 'http://source.jalview.org/git/jalview.git'. simple 20-Nov-2024 00:00:02 Checking out revision 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9. simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/RNAalifold does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/VamJalview does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/hmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/mchmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/jalview-headless does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/clinvar does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/jim does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/kira does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/koen does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/mungo does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/phyre does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/thomas does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/spikes/toch does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/remotes/origin/vamsasDemo does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 20-Nov-2024 00:00:02 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/RNAalifold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/VamJalview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jalview-headless does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/clinvar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/kira does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/koen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/phyre does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/thomas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/toch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/vamsasDemo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/RNAalifold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/VamJalview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jalview-headless does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/clinvar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/kira does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/koen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/phyre does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/thomas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/toch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/vamsasDemo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/RNAalifold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/VamJalview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jalview-headless does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/clinvar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/kira does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/koen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/phyre does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/thomas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/toch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/vamsasDemo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 20-Nov-2024 00:00:03 * [new branch] features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115 simple 20-Nov-2024 00:00:03 * [new branch] spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/RNAalifold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/VamJalview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jalview-headless does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/clinvar does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/phyre2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/jim does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/kira does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/koen does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/mungo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/phyre does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/thomas does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/spikes/toch does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/remotes/origin/vamsasDemo does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 20-Nov-2024 00:00:03 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 20-Nov-2024 00:00:10 Already on 'releases/Release_2_11_4_Branch' simple 20-Nov-2024 00:00:10 Updated source code to revision: 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9 simple 20-Nov-2024 00:00:10 Finished task 'Checkout Default Repository' with result: Success simple 20-Nov-2024 00:00:10 Running pre-build action: VCS Version Collector simple 20-Nov-2024 00:00:10 Running pre-build action: Artifactory Release Staging command 20-Nov-2024 00:00:11 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE command 20-Nov-2024 00:00:11 Substituting variable: ${bamboo.planKey} with JB-GTC0 simple 20-Nov-2024 00:00:11 Starting task 'Jalview ${bamboo.CHANNEL} distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 20-Nov-2024 00:00:11 Bamboo Artifactory Plugin version: 2.6.2 command 20-Nov-2024 00:00:11 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GTC0 clean getdown shadowJar\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_repository_46497969_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GTC0-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=29\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nSHLVL=1\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 20-Nov-2024 00:00:18 Starting a Gradle Daemon (subsequent builds will be faster) build 20-Nov-2024 00:00:37 build 20-Nov-2024 00:00:37 > Configure project : build 20-Nov-2024 00:00:37 Using properties from file './utils/channels/test-release/channel_gradle.properties' build 20-Nov-2024 00:00:37 JALVIEW_VERSION is set to '2.11.4.1' build 20-Nov-2024 00:00:37 HEADLESS BUILD build 20-Nov-2024 00:00:37 J2S ENABLED build 20-Nov-2024 00:00:37 Setting jalviewjs_ignore_transpile_errors to 'false' build 20-Nov-2024 00:00:37 Using a TEST-RELEASE profile. build 20-Nov-2024 00:00:39 eclipseDir exists build 20-Nov-2024 00:00:40 build 20-Nov-2024 00:00:40 > Task :clean build 20-Nov-2024 00:00:40 > Task :cleanPackageDir build 20-Nov-2024 00:00:41 > Task :getdownImagesCopy build 20-Nov-2024 00:00:41 > Task :getdownImagesProcess build 20-Nov-2024 00:00:41 > Task :getdownImages build 20-Nov-2024 00:00:46 > Task :copyHelp build 20-Nov-2024 00:00:51 > Task :buildIndices build 20-Nov-2024 00:00:52 > Task :copyResources build 20-Nov-2024 00:00:52 > Task :copyChannelResources build 20-Nov-2024 00:00:53 build 20-Nov-2024 00:00:53 > Task :createBuildProperties build 20-Nov-2024 00:00:53 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 20-Nov-2024 00:00:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:00:53 build 20-Nov-2024 00:00:53 > Task :buildResources build 20-Nov-2024 00:00:53 > Task :copyDocs build 20-Nov-2024 00:00:54 build 20-Nov-2024 00:00:54 > Task :convertMdFiles build 20-Nov-2024 00:00:54 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 20-Nov-2024 00:00:54 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/releaseprocess.html build 20-Nov-2024 00:00:54 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 20-Nov-2024 00:00:54 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/building.html build 20-Nov-2024 00:00:54 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/jalview-projects.html build 20-Nov-2024 00:00:55 build 20-Nov-2024 00:00:55 > Task :releasesTemplates build 20-Nov-2024 00:00:55 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 20-Nov-2024 00:00:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:00:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:00:55 Stripping rc/test/etc for 2_11_4_1-test build 20-Nov-2024 00:00:55 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md build 20-Nov-2024 00:00:55 build 20-Nov-2024 00:00:55 > Task :prepare build 20-Nov-2024 00:00:57 build 20-Nov-2024 00:00:57 > Task :compileJava build 20-Nov-2024 00:00:57 Setting target compatibility to 11 error 20-Nov-2024 00:01:29 Note: Some input files use or override a deprecated API. error 20-Nov-2024 00:01:29 Note: Recompile with -Xlint:deprecation for details. error 20-Nov-2024 00:01:29 Note: Some input files use unchecked or unsafe operations. error 20-Nov-2024 00:01:29 Note: Recompile with -Xlint:unchecked for details. build 20-Nov-2024 00:01:33 build 20-Nov-2024 00:01:33 > Task :processResources build 20-Nov-2024 00:01:33 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:33 build 20-Nov-2024 00:01:33 > Task :classes build 20-Nov-2024 00:01:35 build 20-Nov-2024 00:01:35 > Task :compileLinkCheck build 20-Nov-2024 00:01:35 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 20-Nov-2024 00:01:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:01:37 build 20-Nov-2024 00:01:37 > Task :linkCheck build 20-Nov-2024 00:01:37 Checking help file links build 20-Nov-2024 00:03:42 build 20-Nov-2024 00:03:42 Results: build 20-Nov-2024 00:03:42 159 distinct help targets build 20-Nov-2024 00:03:42 159 help mappings build 20-Nov-2024 00:03:42 0 invalid targets build 20-Nov-2024 00:03:42 32 unused targets build 20-Nov-2024 00:03:42 uniprotfetcher: html/features/uniprotsequencefetcher.html build 20-Nov-2024 00:03:42 overviewprefs: html/features/preferences.html#overview build 20-Nov-2024 00:03:42 cdnafeatures: html/features/codingfeatures.html build 20-Nov-2024 00:03:42 startupprefs: html/features/preferences.html#startup build 20-Nov-2024 00:03:42 ensemblfetch: html/features/ensemblsequencefetcher.html build 20-Nov-2024 00:03:42 io.modellerpir: html/io/modellerpir.html build 20-Nov-2024 00:03:42 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 20-Nov-2024 00:03:42 pdbmcviewer: html/features/pdbviewer.html build 20-Nov-2024 00:03:42 workingwithpae: html/features/paematrices.html build 20-Nov-2024 00:03:42 groovy.colours: html/features/groovy.html#groovyColours build 20-Nov-2024 00:03:42 seqmappings: html/features/seqmappings.html build 20-Nov-2024 00:03:42 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 20-Nov-2024 00:03:42 splitframe.mirrorfonts: html/features/splitView.html#mirror build 20-Nov-2024 00:03:42 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 20-Nov-2024 00:03:42 search: html/features/search.html build 20-Nov-2024 00:03:42 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 20-Nov-2024 00:03:42 alformats: html/io/fileformats.html build 20-Nov-2024 00:03:42 strucprefs: html/features/preferences.html#structure build 20-Nov-2024 00:03:42 siftsmapping: html/features/siftsmapping.html build 20-Nov-2024 00:03:42 chimera.annotxfer: html/features/chimera.html#annotxfer build 20-Nov-2024 00:03:42 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 20-Nov-2024 00:03:42 newkeys: html/features/newkeystrokes.html build 20-Nov-2024 00:03:42 importvcf.attribs: html/features/importvcf.html#attribs build 20-Nov-2024 00:03:42 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 20-Nov-2024 00:03:42 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 20-Nov-2024 00:03:42 jalarchive: html/features/jalarchive.html build 20-Nov-2024 00:03:42 newsreader: html/webServices/newsreader.html build 20-Nov-2024 00:03:42 jalviewcltool: html/features/commandline.html#script build 20-Nov-2024 00:03:42 popMenuAddref: html/menus/popupMenu.html#addrefannot build 20-Nov-2024 00:03:42 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 20-Nov-2024 00:03:42 paematrixformat: html/io/paematrixformat.html build 20-Nov-2024 00:03:42 overview: html/features/overview.html build 20-Nov-2024 00:03:42 0 invalid map urls build 20-Nov-2024 00:03:42 0 invalid image attributes build 20-Nov-2024 00:03:42 508 internal href links (110 with anchors) build 20-Nov-2024 00:03:42 0 invalid internal href links build 20-Nov-2024 00:03:42 0 invalid internal anchor links build 20-Nov-2024 00:03:42 113 external href links build 20-Nov-2024 00:03:42 External links not verified as internet not available build 20-Nov-2024 00:03:42 *** Success *** build 20-Nov-2024 00:03:43 build 20-Nov-2024 00:03:43 > Task :jar build 20-Nov-2024 00:03:46 > Task :syncJars build 20-Nov-2024 00:03:46 > Task :makeDist build 20-Nov-2024 00:03:46 > Task :getdownWebsiteBuild build 20-Nov-2024 00:03:48 build 20-Nov-2024 00:03:48 > Task :getdownDigest build 20-Nov-2024 00:03:48 Generating digest file './build/website/docroot/getdown/test-release/11/digest.txt'... build 20-Nov-2024 00:03:48 Generating digest file './build/website/docroot/getdown/test-release/11/digest2.txt'... build 20-Nov-2024 00:03:48 build 20-Nov-2024 00:03:48 > Task :getdown build 20-Nov-2024 00:03:48 LIKELY RSYNC COMMAND: build 20-Nov-2024 00:03:48 mkdir -p '/Volumes/jalview/docroot/getdown/test-release/11/' build 20-Nov-2024 00:03:48 rsync -avh --delete './build/website/docroot/getdown/test-release/11/' '/Volumes/jalview/docroot/getdown/test-release/11/' error 20-Nov-2024 00:03:48 2024/11/20 00:03:46:767 WARNING Starting without install4j classes error 20-Nov-2024 00:03:48 2024/11/20 00:03:47:315 WARNING Starting without install4j classes build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 > Task :shadowJar build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 20-Nov-2024 00:03:56 Please consult deprecation warnings for more details. build 20-Nov-2024 00:03:56 build 20-Nov-2024 00:03:56 BUILD SUCCESSFUL in 3m 45s build 20-Nov-2024 00:03:56 22 actionable tasks: 22 executed simple 20-Nov-2024 00:03:57 Finished task 'Jalview ${bamboo.CHANNEL} distribution for Java 11' with result: Success command 20-Nov-2024 00:03:57 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE command 20-Nov-2024 00:03:57 Substituting variable: ${bamboo.planKey} with JB-GTC0 simple 20-Nov-2024 00:03:57 Starting task 'Jalview 1.8 build' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 20-Nov-2024 00:03:57 Bamboo Artifactory Plugin version: 2.6.2 command 20-Nov-2024 00:03:57 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=1.8 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 getdown shadowJar\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: 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Git\nLOGNAME=bamboo\nbamboo_buildNumber=29\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nSHLVL=1\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_name=Jalview 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shadowJar\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 20-Nov-2024 00:03:58 build 20-Nov-2024 00:03:58 > Configure project : build 20-Nov-2024 00:03:58 Using properties from file './utils/channels/test-release/channel_gradle.properties' build 20-Nov-2024 00:03:58 JALVIEW_VERSION is set to '2.11.4.1' build 20-Nov-2024 00:03:58 HEADLESS BUILD build 20-Nov-2024 00:03:58 J2S ENABLED build 20-Nov-2024 00:03:58 Setting jalviewjs_ignore_transpile_errors to 'false' build 20-Nov-2024 00:03:58 Using a TEST-RELEASE profile. build 20-Nov-2024 00:03:58 eclipseDir exists build 20-Nov-2024 00:03:58 build 20-Nov-2024 00:03:58 > Task :getdownImagesCopy build 20-Nov-2024 00:03:58 > Task :getdownImagesProcess build 20-Nov-2024 00:03:58 > Task :getdownImages build 20-Nov-2024 00:03:58 > Task :cleanPackageDir build 20-Nov-2024 00:03:58 > Task :copyHelp UP-TO-DATE build 20-Nov-2024 00:04:00 > Task :buildIndices build 20-Nov-2024 00:04:00 > Task :copyResources UP-TO-DATE build 20-Nov-2024 00:04:00 > Task :copyChannelResources UP-TO-DATE build 20-Nov-2024 00:04:00 build 20-Nov-2024 00:04:00 > Task :createBuildProperties build 20-Nov-2024 00:04:00 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 20-Nov-2024 00:04:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:00 build 20-Nov-2024 00:04:00 > Task :buildResources build 20-Nov-2024 00:04:00 > Task :copyDocs build 20-Nov-2024 00:04:00 build 20-Nov-2024 00:04:00 > Task :convertMdFiles build 20-Nov-2024 00:04:00 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 20-Nov-2024 00:04:00 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/releaseprocess.html build 20-Nov-2024 00:04:00 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 20-Nov-2024 00:04:00 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/building.html build 20-Nov-2024 00:04:00 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build/doc/jalview-projects.html build 20-Nov-2024 00:04:00 build 20-Nov-2024 00:04:00 > Task :releasesTemplates build 20-Nov-2024 00:04:00 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 20-Nov-2024 00:04:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:00 Stripping rc/test/etc for 2_11_4_1-test build 20-Nov-2024 00:04:00 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md build 20-Nov-2024 00:04:00 build 20-Nov-2024 00:04:00 > Task :prepare build 20-Nov-2024 00:04:02 build 20-Nov-2024 00:04:02 > Task :compileJava build 20-Nov-2024 00:04:02 Setting target compatibility to 1.8 error 20-Nov-2024 00:04:09 Note: Some input files use or override a deprecated API. error 20-Nov-2024 00:04:09 Note: Recompile with -Xlint:deprecation for details. error 20-Nov-2024 00:04:09 Note: Some input files use unchecked or unsafe operations. error 20-Nov-2024 00:04:09 Note: Recompile with -Xlint:unchecked for details. build 20-Nov-2024 00:04:13 build 20-Nov-2024 00:04:13 > Task :processResources build 20-Nov-2024 00:04:13 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:13 build 20-Nov-2024 00:04:13 > Task :classes build 20-Nov-2024 00:04:14 build 20-Nov-2024 00:04:14 > Task :compileLinkCheck build 20-Nov-2024 00:04:14 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 20-Nov-2024 00:04:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:04:16 build 20-Nov-2024 00:04:16 > Task :linkCheck build 20-Nov-2024 00:04:16 Checking help file links build 20-Nov-2024 00:06:22 build 20-Nov-2024 00:06:22 Results: build 20-Nov-2024 00:06:22 159 distinct help targets build 20-Nov-2024 00:06:22 159 help mappings build 20-Nov-2024 00:06:22 0 invalid targets build 20-Nov-2024 00:06:22 32 unused targets build 20-Nov-2024 00:06:22 uniprotfetcher: html/features/uniprotsequencefetcher.html build 20-Nov-2024 00:06:22 overviewprefs: html/features/preferences.html#overview build 20-Nov-2024 00:06:22 cdnafeatures: html/features/codingfeatures.html build 20-Nov-2024 00:06:22 startupprefs: html/features/preferences.html#startup build 20-Nov-2024 00:06:22 ensemblfetch: html/features/ensemblsequencefetcher.html build 20-Nov-2024 00:06:22 io.modellerpir: html/io/modellerpir.html build 20-Nov-2024 00:06:22 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 20-Nov-2024 00:06:22 pdbmcviewer: html/features/pdbviewer.html build 20-Nov-2024 00:06:22 workingwithpae: html/features/paematrices.html build 20-Nov-2024 00:06:22 groovy.colours: html/features/groovy.html#groovyColours build 20-Nov-2024 00:06:22 seqmappings: html/features/seqmappings.html build 20-Nov-2024 00:06:22 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 20-Nov-2024 00:06:22 splitframe.mirrorfonts: html/features/splitView.html#mirror build 20-Nov-2024 00:06:22 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 20-Nov-2024 00:06:22 search: html/features/search.html build 20-Nov-2024 00:06:22 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 20-Nov-2024 00:06:22 alformats: html/io/fileformats.html build 20-Nov-2024 00:06:22 strucprefs: html/features/preferences.html#structure build 20-Nov-2024 00:06:22 siftsmapping: html/features/siftsmapping.html build 20-Nov-2024 00:06:22 chimera.annotxfer: html/features/chimera.html#annotxfer build 20-Nov-2024 00:06:22 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 20-Nov-2024 00:06:22 newkeys: html/features/newkeystrokes.html build 20-Nov-2024 00:06:22 importvcf.attribs: html/features/importvcf.html#attribs build 20-Nov-2024 00:06:22 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 20-Nov-2024 00:06:22 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 20-Nov-2024 00:06:22 jalarchive: html/features/jalarchive.html build 20-Nov-2024 00:06:22 newsreader: html/webServices/newsreader.html build 20-Nov-2024 00:06:22 jalviewcltool: html/features/commandline.html#script build 20-Nov-2024 00:06:22 popMenuAddref: html/menus/popupMenu.html#addrefannot build 20-Nov-2024 00:06:22 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 20-Nov-2024 00:06:22 paematrixformat: html/io/paematrixformat.html build 20-Nov-2024 00:06:22 overview: html/features/overview.html build 20-Nov-2024 00:06:22 0 invalid map urls build 20-Nov-2024 00:06:22 0 invalid image attributes build 20-Nov-2024 00:06:22 508 internal href links (110 with anchors) build 20-Nov-2024 00:06:22 0 invalid internal href links build 20-Nov-2024 00:06:22 0 invalid internal anchor links build 20-Nov-2024 00:06:22 113 external href links build 20-Nov-2024 00:06:22 External links not verified as internet not available build 20-Nov-2024 00:06:22 *** Success *** build 20-Nov-2024 00:06:22 build 20-Nov-2024 00:06:22 > Task :jar build 20-Nov-2024 00:06:27 > Task :syncJars build 20-Nov-2024 00:06:27 > Task :makeDist build 20-Nov-2024 00:06:27 > Task :getdownWebsiteBuild build 20-Nov-2024 00:06:28 build 20-Nov-2024 00:06:28 > Task :getdownDigest error 20-Nov-2024 00:06:28 2024/11/20 00:06:27:504 WARNING Starting without install4j classes error 20-Nov-2024 00:06:28 2024/11/20 00:06:27:996 WARNING Starting without install4j classes build 20-Nov-2024 00:06:28 Generating digest file './build/website/docroot/getdown/test-release/1.8/digest.txt'... build 20-Nov-2024 00:06:28 Generating digest file './build/website/docroot/getdown/test-release/1.8/digest2.txt'... build 20-Nov-2024 00:06:28 build 20-Nov-2024 00:06:28 > Task :getdown build 20-Nov-2024 00:06:28 LIKELY RSYNC COMMAND: build 20-Nov-2024 00:06:28 mkdir -p '/Volumes/jalview/docroot/getdown/test-release/1.8/' build 20-Nov-2024 00:06:28 rsync -avh --delete './build/website/docroot/getdown/test-release/1.8/' '/Volumes/jalview/docroot/getdown/test-release/1.8/' build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 > Task :shadowJar build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 20-Nov-2024 00:06:35 Please consult deprecation warnings for more details. build 20-Nov-2024 00:06:35 build 20-Nov-2024 00:06:35 BUILD SUCCESSFUL in 2m 38s build 20-Nov-2024 00:06:35 21 actionable tasks: 18 executed, 3 up-to-date simple 20-Nov-2024 00:06:35 Finished task 'Jalview 1.8 build' with result: Success command 20-Nov-2024 00:06:35 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE command 20-Nov-2024 00:06:35 Substituting variable: ${bamboo.planKey} with JB-GTC0 simple 20-Nov-2024 00:06:35 Starting task 'JalviewJS ${bamboo.CHANNEL} release' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 20-Nov-2024 00:06:35 Bamboo Artifactory Plugin version: 2.6.2 command 20-Nov-2024 00:06:35 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 --info eclipse jalviewjsCreateJ2sSettings jalviewjs\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_repository_46497969_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GTC0-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=29\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nSHLVL=1\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GTC0 clean getdown shadowJar\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_8=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=1.8 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 getdown shadowJar\nHOME=/home/bamboo\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 20-Nov-2024 00:06:36 Initialized native services in: /srv/bamboo/home/bamboo/.gradle/native build 20-Nov-2024 00:06:36 Initialized jansi services in: /srv/bamboo/home/bamboo/.gradle/native build 20-Nov-2024 00:06:36 The client will now receive all logging from the daemon (pid: 8694). The daemon log file: /srv/bamboo/home/bamboo/.gradle/daemon/7.4.2/daemon-8694.out.log build 20-Nov-2024 00:06:36 Starting 3rd build in daemon [uptime: 6 mins 13.141 secs, performance: 100%, non-heap usage: 34% of 256 MiB] build 20-Nov-2024 00:06:36 Using 4 worker leases. build 20-Nov-2024 00:06:36 Watching the file system is configured to be enabled if available build 20-Nov-2024 00:06:36 File system watching is inactive build 20-Nov-2024 00:06:36 Starting Build build 20-Nov-2024 00:06:36 Settings evaluated using settings file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/settings.gradle'. build 20-Nov-2024 00:06:36 Projects loaded. Root project using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build.gradle'. build 20-Nov-2024 00:06:36 Included projects: [root project 'jalview'] build 20-Nov-2024 00:06:36 build 20-Nov-2024 00:06:36 > Configure project : build 20-Nov-2024 00:06:36 Evaluating root project 'jalview' using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build.gradle'. build 20-Nov-2024 00:06:36 Using properties from file './utils/channels/test-release/channel_gradle.properties' build 20-Nov-2024 00:06:36 JALVIEW_VERSION is set to '2.11.4.1' build 20-Nov-2024 00:06:36 HEADLESS BUILD build 20-Nov-2024 00:06:36 J2S ENABLED build 20-Nov-2024 00:06:36 Setting jalviewjs_ignore_transpile_errors to 'false' build 20-Nov-2024 00:06:36 Using a TEST-RELEASE profile. build 20-Nov-2024 00:06:36 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/main/java', not found build 20-Nov-2024 00:06:36 eclipseDir exists build 20-Nov-2024 00:06:36 All projects evaluated. build 20-Nov-2024 00:06:36 Selected primary task 'eclipse' from project : build 20-Nov-2024 00:06:36 Selected primary task 'jalviewjsCreateJ2sSettings' from project : build 20-Nov-2024 00:06:36 Selected primary task 'jalviewjs' from project : build 20-Nov-2024 00:06:36 Tasks to be executed: [task ':eclipseClasspath', task ':eclipseJdt', task ':eclipseProject', task ':eclipse', task ':jalviewjsCreateJ2sSettings', task ':jalviewjsEclipsePaths', task ':jalviewjsEclipseCopyDropins', task ':jalviewjsSetEclipseWorkspace', task ':jalviewjsEclipseSetup', task ':jalviewjsEnableAltFileProperty', task ':eclipseSetup', task ':jalviewjsProjectImport', task ':jalviewjsTranspile', task ':jalviewjsCopyTransferSiteJs', task ':jalviewjsTransferUnzipLib', task ':jalviewjsTransferUnzipSwingJs', task ':jalviewjsTransferUnzipAllLibs', task ':jalviewjsSyncAllLibs', task ':copyResources', task ':createBuildProperties', task ':jalviewjsSyncBuildProperties', task ':jalviewjsBuildAllCores', task ':jalviewjsPublishCoreTemplates', task ':jalviewjsSyncCore', task ':copyChannelResources', task ':buildResources', task ':jalviewjsSyncResources', task ':jalviewjsSyncSiteResources', task ':jalviewjsPrepareSite', task ':jalviewjsBuildSite', task ':cleanJalviewjsChromiumUserDir', task ':jalviewjsChromiumProfile', task ':jalviewjsCopyStderrLaunchFile', task ':jalviewjsLaunchTest', task ':jalviewjs'] build 20-Nov-2024 00:06:36 Tasks that were excluded: [] build 20-Nov-2024 00:06:36 :eclipseClasspath (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :eclipseClasspath build 20-Nov-2024 00:06:37 Caching disabled for task ':eclipseClasspath' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':eclipseClasspath' is not up-to-date because: build 20-Nov-2024 00:06:37 Task.upToDateWhen is false. build 20-Nov-2024 00:06:37 :eclipseClasspath (Thread[Execution worker for ':',5,main]) completed. Took 0.411 secs. build 20-Nov-2024 00:06:37 :eclipseJdt (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :eclipseJdt build 20-Nov-2024 00:06:37 Caching disabled for task ':eclipseJdt' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':eclipseJdt' is not up-to-date because: build 20-Nov-2024 00:06:37 Task.upToDateWhen is false. build 20-Nov-2024 00:06:37 :eclipseJdt (Thread[Execution worker for ':',5,main]) completed. Took 0.111 secs. build 20-Nov-2024 00:06:37 :eclipseProject (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :eclipseProject build 20-Nov-2024 00:06:37 Caching disabled for task ':eclipseProject' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':eclipseProject' is not up-to-date because: build 20-Nov-2024 00:06:37 Task.upToDateWhen is false. build 20-Nov-2024 00:06:37 :eclipseProject (Thread[Execution worker for ':',5,main]) completed. Took 0.007 secs. build 20-Nov-2024 00:06:37 :eclipse (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :eclipse build 20-Nov-2024 00:06:37 Skipping task ':eclipse' as it has no actions. build 20-Nov-2024 00:06:37 :eclipse (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:06:37 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsCreateJ2sSettings build 20-Nov-2024 00:06:37 Caching disabled for task ':jalviewjsCreateJ2sSettings' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':jalviewjsCreateJ2sSettings' is not up-to-date because: build 20-Nov-2024 00:06:37 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/config/j2s has been removed. build 20-Nov-2024 00:06:37 Output property 'outputFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/config/j2s has been removed. build 20-Nov-2024 00:06:37 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) completed. Took 0.002 secs. build 20-Nov-2024 00:06:37 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsEclipsePaths build 20-Nov-2024 00:06:37 Caching disabled for task ':jalviewjsEclipsePaths' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':jalviewjsEclipsePaths' is not up-to-date because: build 20-Nov-2024 00:06:37 Task has not declared any outputs despite executing actions. build 20-Nov-2024 00:06:37 Running task jalviewjsEclipsePaths as IN_ECLIPSE=false build 20-Nov-2024 00:06:37 ECLIPSE VERSION=4.28.0 build 20-Nov-2024 00:06:37 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) completed. Took 0.001 secs. build 20-Nov-2024 00:06:37 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsEclipseCopyDropins build 20-Nov-2024 00:06:37 Caching disabled for task ':jalviewjsEclipseCopyDropins' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':jalviewjsEclipseCopyDropins' is not up-to-date because: build 20-Nov-2024 00:06:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/eclipse_dropins has been removed. build 20-Nov-2024 00:06:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/eclipse_dropins/com.seeq.eclipse.importprojects.jar has been removed. build 20-Nov-2024 00:06:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/eclipse_dropins/net.sf.j2s.core-j11.jar has been removed. build 20-Nov-2024 00:06:37 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) completed. Took 0.044 secs. build 20-Nov-2024 00:06:37 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsSetEclipseWorkspace build 20-Nov-2024 00:06:37 Caching disabled for task ':jalviewjsSetEclipseWorkspace' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Task ':jalviewjsSetEclipseWorkspace' is not up-to-date because: build 20-Nov-2024 00:06:37 Task.upToDateWhen is false. build 20-Nov-2024 00:06:37 Running task jalviewjsSetEclipseWorkspace as IN_ECLIPSE=false build 20-Nov-2024 00:06:37 NEW ECLIPSE WORKSPACE: /tmp/groovy-generated-tmpdir-17966073357557657537 build 20-Nov-2024 00:06:37 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 20-Nov-2024 00:06:37 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsEclipseSetup build 20-Nov-2024 00:06:37 Skipping task ':jalviewjsEclipseSetup' as it has no actions. build 20-Nov-2024 00:06:37 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:06:37 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :jalviewjsEnableAltFileProperty UP-TO-DATE build 20-Nov-2024 00:06:37 Caching disabled for task ':jalviewjsEnableAltFileProperty' because: build 20-Nov-2024 00:06:37 Build cache is disabled build 20-Nov-2024 00:06:37 Skipping task ':jalviewjsEnableAltFileProperty' as it is up-to-date. build 20-Nov-2024 00:06:37 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:06:37 :eclipseSetup (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:37 build 20-Nov-2024 00:06:37 > Task :eclipseSetup build 20-Nov-2024 00:06:37 Skipping task ':eclipseSetup' as it has no actions. build 20-Nov-2024 00:06:37 :eclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:06:37 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:06:39 build 20-Nov-2024 00:06:39 > Task :jalviewjsProjectImport build 20-Nov-2024 00:06:39 Caching disabled for task ':jalviewjsProjectImport' because: build 20-Nov-2024 00:06:39 Build cache is disabled build 20-Nov-2024 00:06:39 Task ':jalviewjsProjectImport' is not up-to-date because: build 20-Nov-2024 00:06:39 Task.upToDateWhen is false. build 20-Nov-2024 00:06:39 Running task jalviewjsProjectImport as IN_ECLIPSE=false build 20-Nov-2024 00:06:39 Starting process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /home/bamboo/buildtools/eclipse/latest/eclipse/eclipse -nosplash --launcher.suppressErrors -application com.seeq.eclipse.importprojects.headlessimport -data /tmp/groovy-generated-tmpdir-17966073357557657537 -import /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 20-Nov-2024 00:06:39 Successfully started process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse'' error 20-Nov-2024 00:06:42 SLF4J: No SLF4J providers were found. error 20-Nov-2024 00:06:42 SLF4J: Defaulting to no-operation (NOP) logger implementation error 20-Nov-2024 00:06:42 SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details. error 20-Nov-2024 00:07:01 Job found still running after platform shutdown. Jobs should be canceled by the plugin that scheduled them during shutdown: org.eclipse.buildship.core.internal.workspace.SynchronizationJob build 20-Nov-2024 00:07:01 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) completed. Took 24.235 secs. build 20-Nov-2024 00:07:01 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:03 build 20-Nov-2024 00:07:03 > Task :jalviewjsTranspile build 20-Nov-2024 00:07:03 Caching disabled for task ':jalviewjsTranspile' because: build 20-Nov-2024 00:07:03 Build cache is disabled build 20-Nov-2024 00:07:03 Task ':jalviewjsTranspile' is not up-to-date because: build 20-Nov-2024 00:07:03 Task.upToDateWhen is false. build 20-Nov-2024 00:07:03 Running task jalviewjsTranspile as IN_ECLIPSE=false build 20-Nov-2024 00:07:03 Starting process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /home/bamboo/buildtools/eclipse/latest/eclipse/eclipse -nosplash --launcher.suppressErrors -application org.eclipse.jdt.apt.core.aptBuild -data /tmp/groovy-generated-tmpdir-17966073357557657537 -cleanBuild jalview --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 20-Nov-2024 00:07:03 Successfully started process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse'' error 20-Nov-2024 00:07:03 SLF4J: No SLF4J providers were found. error 20-Nov-2024 00:07:03 SLF4J: Defaulting to no-operation (NOP) logger implementation error 20-Nov-2024 00:07:03 SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details. build 20-Nov-2024 00:07:04 Invoking 'Java Builder' on '/jalview'. build 20-Nov-2024 00:07:06 net.sf.j2s.core.3.3.1/3.3.1-v1 started build 20-Nov-2024 00:07:06 J2S CompilationParticipant started build 20-Nov-2024 00:07:06 J2S isActive true /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:06 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:07 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:07 Cleaning output folder for jalview build 20-Nov-2024 00:07:07 Build done build 20-Nov-2024 00:07:07 Invoking 'Gradle Project Builder' on '/jalview'. build 20-Nov-2024 00:07:07 Invoking 'Java Builder' on '/jalview'. build 20-Nov-2024 00:07:07 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:07 Preparing to build jalview build 20-Nov-2024 00:07:07 Cleaning output folder for jalview build 20-Nov-2024 00:07:07 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:07 Copying resources to the output folder build 20-Nov-2024 00:07:07 Analyzing sources build 20-Nov-2024 00:07:07 J2S buildStarting 1103 files, contexts.size() = 1, isBatch=true build 20-Nov-2024 00:07:07 Compiling jalview/src/com/github/reinert/jjschema build 20-Nov-2024 00:07:09 Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 1 warning) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 2 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 3 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 4 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 5 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 9 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 12 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 13 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 14 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 15 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 37 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 38 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 46 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 47 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 48 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 49 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 50 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 51 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 52 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 59 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 63 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 67 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 69 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 89 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 90 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 91 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 98 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 108 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 113 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 114 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 115 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 119 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat build 20-Nov-2024 00:07:09 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat/wrap build 20-Nov-2024 00:07:09 (Found 124 warnings) Compiling jalview/src/darrylbu/util build 20-Nov-2024 00:07:09 (Found 124 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 20-Nov-2024 00:07:09 (Found 126 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 20-Nov-2024 00:07:09 (Found 133 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 20-Nov-2024 00:07:09 (Found 136 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2/port build 20-Nov-2024 00:07:09 (Found 136 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:09 (Found 143 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:09 (Found 150 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:09 (Found 188 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:09 (Found 195 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:09 (Found 251 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 283 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 290 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 358 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 361 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 364 warnings) Compiling jalview/src/ext/vamsas build 20-Nov-2024 00:07:10 (Found 366 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 370 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 375 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 380 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 413 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 421 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 422 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 423 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 424 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 426 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 427 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 428 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 434 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 441 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 467 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 471 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 472 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 507 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 571 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 572 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 578 warnings) Compiling jalview/src/jalview/analysis build 20-Nov-2024 00:07:10 (Found 578 warnings) Compiling jalview/src/jalview/analysis/scoremodels build 20-Nov-2024 00:07:10 (Found 581 warnings) Compiling jalview/src/jalview/analysis/scoremodels build 20-Nov-2024 00:07:10 (Found 591 warnings) Compiling jalview/src/jalview/analytics build 20-Nov-2024 00:07:10 (Found 591 warnings) Compiling jalview/src/jalview/api build 20-Nov-2024 00:07:10 (Found 591 warnings) Compiling jalview/src/jalview/api/analysis build 20-Nov-2024 00:07:10 (Found 593 warnings) Compiling jalview/src/jalview/api/structures build 20-Nov-2024 00:07:10 (Found 596 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 652 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 661 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 662 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 667 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 668 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 670 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 681 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 683 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 688 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 689 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 690 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 691 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 693 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 695 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 696 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 698 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 699 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 704 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 705 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 706 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 708 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 709 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 711 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:10 (Found 719 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 729 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 730 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 731 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 733 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 734 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 739 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 742 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 779 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 781 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 782 warnings) Compiling jalview/src/jalview/appletgui build 20-Nov-2024 00:07:11 (Found 782 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 786 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 789 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 790 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 797 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 799 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 3 errors + 857 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 3 errors + 862 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 3 errors + 864 warnings) Compiling jalview/src/jalview/bin build 20-Nov-2024 00:07:11 (Found 3 errors + 864 warnings) Compiling jalview/src/jalview/bin/argparser build 20-Nov-2024 00:07:11 (Found 3 errors + 865 warnings) Compiling jalview/src/jalview/bin/argparser build 20-Nov-2024 00:07:11 (Found 3 errors + 867 warnings) Compiling jalview/src/jalview/bin/argparser build 20-Nov-2024 00:07:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/bin/argparser build 20-Nov-2024 00:07:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/bin/groovy build 20-Nov-2024 00:07:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/commands build 20-Nov-2024 00:07:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/controller build 20-Nov-2024 00:07:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 881 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 882 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 883 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 886 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 887 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 888 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 894 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 898 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 900 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 901 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 902 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 903 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 908 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 909 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 917 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 918 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 919 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 922 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 928 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 932 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 936 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 938 warnings) Compiling jalview/src/jalview/datamodel build 20-Nov-2024 00:07:11 (Found 3 errors + 939 warnings) Compiling jalview/src/jalview/datamodel/annotations build 20-Nov-2024 00:07:11 (Found 3 errors + 939 warnings) Compiling jalview/src/jalview/datamodel/features build 20-Nov-2024 00:07:12 (Found 3 errors + 939 warnings) Compiling jalview/src/jalview/exceptions build 20-Nov-2024 00:07:12 (Found 3 errors + 939 warnings) Compiling jalview/src/jalview/ext/android build 20-Nov-2024 00:07:12 (Found 3 errors + 939 warnings) Compiling jalview/src/jalview/ext/ensembl build 20-Nov-2024 00:07:12 (Found 3 errors + 941 warnings) Compiling jalview/src/jalview/ext/ensembl build 20-Nov-2024 00:07:12 (Found 3 errors + 943 warnings) Compiling jalview/src/jalview/ext/ensembl build 20-Nov-2024 00:07:12 (Found 3 errors + 944 warnings) Compiling jalview/src/jalview/ext/ensembl build 20-Nov-2024 00:07:12 (Found 3 errors + 946 warnings) Compiling jalview/src/jalview/ext/ensembl build 20-Nov-2024 00:07:12 (Found 3 errors + 949 warnings) Compiling jalview/src/jalview/ext/htsjdk build 20-Nov-2024 00:07:12 (Found 3 errors + 950 warnings) Compiling jalview/src/jalview/ext/htsjdk build 20-Nov-2024 00:07:12 (Found 3 errors + 955 warnings) Compiling jalview/src/jalview/ext/jmol build 20-Nov-2024 00:07:12 (Found 3 errors + 959 warnings) Compiling jalview/src/jalview/ext/paradise build 20-Nov-2024 00:07:12 (Found 3 errors + 959 warnings) Compiling jalview/src/jalview/ext/pymol build 20-Nov-2024 00:07:12 (Found 3 errors + 961 warnings) Compiling jalview/src/jalview/ext/pymol build 20-Nov-2024 00:07:12 (Found 3 errors + 961 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 20-Nov-2024 00:07:12 (Found 3 errors + 962 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 20-Nov-2024 00:07:12 (Found 3 errors + 963 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 20-Nov-2024 00:07:12 (Found 3 errors + 963 warnings) Compiling jalview/src/jalview/ext/so build 20-Nov-2024 00:07:12 (Found 3 errors + 963 warnings) Compiling jalview/src/jalview/ext/varna build 20-Nov-2024 00:07:12 (Found 3 errors + 963 warnings) Compiling jalview/src/jalview/fts/api build 20-Nov-2024 00:07:12 (Found 3 errors + 964 warnings) Compiling jalview/src/jalview/fts/api build 20-Nov-2024 00:07:12 (Found 3 errors + 965 warnings) Compiling jalview/src/jalview/fts/core build 20-Nov-2024 00:07:12 (Found 3 errors + 968 warnings) Compiling jalview/src/jalview/fts/core build 20-Nov-2024 00:07:12 (Found 3 errors + 969 warnings) Compiling jalview/src/jalview/fts/core build 20-Nov-2024 00:07:12 (Found 3 errors + 970 warnings) Compiling jalview/src/jalview/fts/core build 20-Nov-2024 00:07:12 (Found 3 errors + 970 warnings) Compiling jalview/src/jalview/fts/service/alphafold build 20-Nov-2024 00:07:12 (Found 3 errors + 970 warnings) Compiling jalview/src/jalview/fts/service/pdb build 20-Nov-2024 00:07:12 (Found 3 errors + 977 warnings) Compiling jalview/src/jalview/fts/service/pdb build 20-Nov-2024 00:07:12 (Found 3 errors + 977 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 20-Nov-2024 00:07:12 (Found 3 errors + 979 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 20-Nov-2024 00:07:12 (Found 3 errors + 983 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 20-Nov-2024 00:07:12 (Found 3 errors + 987 warnings) Compiling jalview/src/jalview/fts/service/uniprot build 20-Nov-2024 00:07:12 (Found 3 errors + 987 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 988 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 990 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 991 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 992 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 993 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 994 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 995 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 996 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1002 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1004 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1005 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1006 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1015 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1045 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1055 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1056 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1057 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:12 (Found 3 errors + 1058 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1063 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1064 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1065 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1070 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1071 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1075 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1080 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1081 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1083 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1084 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1085 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1086 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1087 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1093 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1094 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1095 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1096 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1097 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1099 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1100 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1101 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1104 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1106 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1113 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1115 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1117 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1118 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1119 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1121 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1125 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1134 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1143 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1146 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1147 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1148 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1150 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1151 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1153 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1159 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1162 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:13 (Found 3 errors + 1163 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1201 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1206 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1207 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1234 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1237 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1244 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1302 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1315 warnings) Compiling jalview/src/jalview/gui build 20-Nov-2024 00:07:14 (Found 3 errors + 1317 warnings) Compiling jalview/src/jalview/gui/structurechooser build 20-Nov-2024 00:07:14 (Found 3 errors + 1319 warnings) Compiling jalview/src/jalview/gui/structurechooser build 20-Nov-2024 00:07:14 (Found 3 errors + 1324 warnings) Compiling jalview/src/jalview/gui/structurechooser build 20-Nov-2024 00:07:14 (Found 3 errors + 1324 warnings) Compiling jalview/src/jalview/httpserver build 20-Nov-2024 00:07:14 (Found 3 errors + 1324 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1329 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1331 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1333 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1335 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1355 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1357 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1359 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1363 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1366 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1367 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1368 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1369 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1407 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1410 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1412 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1432 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1465 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1467 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1469 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1470 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1471 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1484 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1546 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1547 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1548 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1630 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1635 warnings) Compiling jalview/src/jalview/io build 20-Nov-2024 00:07:14 (Found 3 errors + 1635 warnings) Compiling jalview/src/jalview/io/cache build 20-Nov-2024 00:07:14 (Found 3 errors + 1636 warnings) Compiling jalview/src/jalview/io/exceptions build 20-Nov-2024 00:07:14 (Found 3 errors + 1636 warnings) Compiling jalview/src/jalview/io/gff build 20-Nov-2024 00:07:14 (Found 3 errors + 1637 warnings) Compiling jalview/src/jalview/io/gff build 20-Nov-2024 00:07:14 (Found 3 errors + 1637 warnings) Compiling jalview/src/jalview/io/packed build 20-Nov-2024 00:07:14 (Found 3 errors + 1643 warnings) Compiling jalview/src/jalview/io/packed build 20-Nov-2024 00:07:14 (Found 3 errors + 1645 warnings) Compiling jalview/src/jalview/io/packed build 20-Nov-2024 00:07:14 (Found 3 errors + 1645 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1663 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1674 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1675 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1688 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1692 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1696 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1719 warnings) Compiling jalview/src/jalview/io/vamsas build 20-Nov-2024 00:07:14 (Found 3 errors + 1722 warnings) Compiling jalview/src/jalview/io/vcf build 20-Nov-2024 00:07:14 (Found 4 errors + 1731 warnings) Compiling jalview/src/jalview/javascript build 20-Nov-2024 00:07:14 (Found 4 errors + 1735 warnings) Compiling jalview/src/jalview/javascript build 20-Nov-2024 00:07:14 (Found 4 errors + 1736 warnings) Compiling jalview/src/jalview/javascript/json build 20-Nov-2024 00:07:14 (Found 4 errors + 1736 warnings) Compiling jalview/src/jalview/javascript/web build 20-Nov-2024 00:07:14 (Found 4 errors + 1737 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:14 (Found 4 errors + 1738 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:14 (Found 4 errors + 1739 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:14 (Found 4 errors + 1742 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1743 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1744 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1745 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1746 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1749 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1751 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1759 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1760 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1761 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1766 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1768 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1769 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1772 warnings) Compiling jalview/src/jalview/jbgui build 20-Nov-2024 00:07:15 (Found 4 errors + 1772 warnings) Compiling jalview/src/jalview/json/binding/biojs build 20-Nov-2024 00:07:15 (Found 4 errors + 1772 warnings) Compiling jalview/src/jalview/json/binding/biojson/v1 build 20-Nov-2024 00:07:15 (Found 4 errors + 1775 warnings) Compiling jalview/src/jalview/log build 20-Nov-2024 00:07:15 (Found 4 errors + 1777 warnings) Compiling jalview/src/jalview/log build 20-Nov-2024 00:07:15 (Found 4 errors + 1778 warnings) Compiling jalview/src/jalview/log build 20-Nov-2024 00:07:15 (Found 4 errors + 1778 warnings) Compiling jalview/src/jalview/math build 20-Nov-2024 00:07:15 (Found 4 errors + 1779 warnings) Compiling jalview/src/jalview/math build 20-Nov-2024 00:07:15 (Found 4 errors + 1780 warnings) Compiling jalview/src/jalview/math build 20-Nov-2024 00:07:15 (Found 4 errors + 1806 warnings) Compiling jalview/src/jalview/project build 20-Nov-2024 00:07:15 (Found 4 errors + 1807 warnings) Compiling jalview/src/jalview/renderer build 20-Nov-2024 00:07:15 (Found 4 errors + 1808 warnings) Compiling jalview/src/jalview/renderer build 20-Nov-2024 00:07:15 (Found 4 errors + 1808 warnings) Compiling jalview/src/jalview/renderer/api build 20-Nov-2024 00:07:15 (Found 4 errors + 1808 warnings) Compiling jalview/src/jalview/renderer/seqfeatures build 20-Nov-2024 00:07:15 (Found 4 errors + 1808 warnings) Compiling jalview/src/jalview/rest build 20-Nov-2024 00:07:15 (Found 4 errors + 1808 warnings) Compiling jalview/src/jalview/schemes build 20-Nov-2024 00:07:15 (Found 4 errors + 1811 warnings) Compiling jalview/src/jalview/schemes build 20-Nov-2024 00:07:15 (Found 4 errors + 1811 warnings) Compiling jalview/src/jalview/structure build 20-Nov-2024 00:07:15 (Found 4 errors + 1812 warnings) Compiling jalview/src/jalview/structure build 20-Nov-2024 00:07:15 (Found 4 errors + 1813 warnings) Compiling jalview/src/jalview/structure build 20-Nov-2024 00:07:15 (Found 4 errors + 1818 warnings) Compiling jalview/src/jalview/structure build 20-Nov-2024 00:07:15 (Found 4 errors + 1819 warnings) Compiling jalview/src/jalview/structures/models build 20-Nov-2024 00:07:15 (Found 4 errors + 1819 warnings) Compiling jalview/src/jalview/urls build 20-Nov-2024 00:07:15 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/urls build 20-Nov-2024 00:07:15 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/urls/api build 20-Nov-2024 00:07:15 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/urls/applet build 20-Nov-2024 00:07:15 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/urls/desktop build 20-Nov-2024 00:07:15 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1821 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1822 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1828 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1829 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1841 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1842 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1846 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1851 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1854 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1855 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1858 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1862 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1866 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1890 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/util/dialogrunner build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/util/imagemaker build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/util build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/util/matcher build 20-Nov-2024 00:07:15 (Found 4 errors + 1891 warnings) Compiling jalview/src/jalview/viewmodel build 20-Nov-2024 00:07:16 (Found 4 errors + 1894 warnings) Compiling jalview/src/jalview/viewmodel build 20-Nov-2024 00:07:16 (Found 4 errors + 1894 warnings) Compiling jalview/src/jalview/viewmodel/annotationfilter build 20-Nov-2024 00:07:16 (Found 4 errors + 1895 warnings) Compiling jalview/src/jalview/viewmodel/seqfeatures build 20-Nov-2024 00:07:16 (Found 4 errors + 1895 warnings) Compiling jalview/src/jalview/viewmodel/styles build 20-Nov-2024 00:07:16 (Found 4 errors + 1895 warnings) Compiling jalview/src/jalview/workers build 20-Nov-2024 00:07:16 (Found 4 errors + 1899 warnings) Compiling jalview/src/jalview/workers build 20-Nov-2024 00:07:16 (Found 4 errors + 1899 warnings) Compiling jalview/src/jalview/ws build 20-Nov-2024 00:07:16 (Found 4 errors + 1901 warnings) Compiling jalview/src/jalview/ws build 20-Nov-2024 00:07:16 (Found 4 errors + 1905 warnings) Compiling jalview/src/jalview/ws build 20-Nov-2024 00:07:16 (Found 4 errors + 1905 warnings) Compiling jalview/src/jalview/ws/datamodel build 20-Nov-2024 00:07:16 (Found 4 errors + 1908 warnings) Compiling jalview/src/jalview/ws/datamodel/alphafold build 20-Nov-2024 00:07:16 (Found 4 errors + 1913 warnings) Compiling jalview/src/jalview/ws/datamodel/alphafold build 20-Nov-2024 00:07:16 (Found 4 errors + 1918 warnings) Compiling jalview/src/jalview/ws/dbsources build 20-Nov-2024 00:07:16 (Found 4 errors + 1919 warnings) Compiling jalview/src/jalview/ws/dbsources build 20-Nov-2024 00:07:16 (Found 4 errors + 1919 warnings) Compiling jalview/src/jalview/ws/ebi build 20-Nov-2024 00:07:16 (Found 4 errors + 1919 warnings) Compiling jalview/src/jalview/ws/io/mime build 20-Nov-2024 00:07:16 (Found 4 errors + 1919 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1923 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1931 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1944 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1958 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1964 warnings) Compiling jalview/src/jalview/ws/jws1 build 20-Nov-2024 00:07:16 (Found 4 errors + 1965 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 1966 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 1976 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 1983 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 1997 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2000 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2004 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2010 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2016 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2028 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2030 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2034 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2060 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2083 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2084 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2089 warnings) Compiling jalview/src/jalview/ws/jws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2095 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 20-Nov-2024 00:07:16 (Found 4 errors + 2099 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 20-Nov-2024 00:07:16 (Found 4 errors + 2102 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 20-Nov-2024 00:07:16 (Found 4 errors + 2113 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 20-Nov-2024 00:07:16 (Found 4 errors + 2120 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 20-Nov-2024 00:07:16 (Found 4 errors + 2120 warnings) Compiling jalview/src/jalview/ws/params build 20-Nov-2024 00:07:16 (Found 4 errors + 2121 warnings) Compiling jalview/src/jalview/ws/params build 20-Nov-2024 00:07:16 (Found 4 errors + 2121 warnings) Compiling jalview/src/jalview/ws/params/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2122 warnings) Compiling jalview/src/jalview/ws/params/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2122 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2123 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2128 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2129 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2130 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2136 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2145 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2151 warnings) Compiling jalview/src/jalview/ws/rest build 20-Nov-2024 00:07:16 (Found 4 errors + 2151 warnings) Compiling jalview/src/jalview/ws/rest/params build 20-Nov-2024 00:07:16 (Found 4 errors + 2154 warnings) Compiling jalview/src/jalview/ws/seqfetcher build 20-Nov-2024 00:07:16 (Found 4 errors + 2154 warnings) Compiling jalview/src/jalview/ws/sifts build 20-Nov-2024 00:07:16 (Found 4 errors + 2156 warnings) Compiling jalview/src/jalview/ws/sifts build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/ws/uimodel build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/ws/utils build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/xml/binding/embl build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/xml/binding/jalview build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/xml/binding/sifts build 20-Nov-2024 00:07:16 (Found 4 errors + 2159 warnings) Compiling jalview/src/jalview/xml/binding/uniprot build 20-Nov-2024 00:07:16 (Found 4 errors + 2166 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2167 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2172 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2179 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2180 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2181 warnings) Compiling jalview/src/mc_view build 20-Nov-2024 00:07:16 (Found 4 errors + 2181 warnings) Compiling jalview/src/org/jibble/epsgraphics build 20-Nov-2024 00:07:16 (Found 4 errors + 2182 warnings) Compiling jalview/src/org/jibble/epsgraphics build 20-Nov-2024 00:07:16 (Found 4 errors + 2188 warnings) Compiling jalview/src/org/jibble/epsgraphics build 20-Nov-2024 00:07:16 (Found 4 errors + 2188 warnings) Compiling jalview/src/org/json build 20-Nov-2024 00:07:16 (Found 4 errors + 2190 warnings) Compiling jalview/src/org/json build 20-Nov-2024 00:07:16 (Found 4 errors + 2191 warnings) Compiling jalview/src/org/json build 20-Nov-2024 00:07:16 (Found 4 errors + 2202 warnings) Compiling jalview/src/org/json/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2208 warnings) Compiling jalview/src/org/json/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2217 warnings) Compiling jalview/src/org/json/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2219 warnings) Compiling jalview/src/org/json/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2221 warnings) Compiling jalview/src/org/json/simple/parser build 20-Nov-2024 00:07:16 (Found 4 errors + 2296 warnings) Compiling jalview/src/org/json/simple/parser build 20-Nov-2024 00:07:16 (Found 4 errors + 2300 warnings) Compiling jalview/src/org/json/simple/parser build 20-Nov-2024 00:07:16 (Found 4 errors + 2300 warnings) Compiling jalview/src/org/stackoverflowusers/file build 20-Nov-2024 00:07:16 (Found 4 errors + 2300 warnings) Compiling jalview/src/swingjs/api build 20-Nov-2024 00:07:16 (Found 4 errors + 2300 warnings) Compiling jalview/src/swingjs/api/js build 20-Nov-2024 00:07:16 (Found 4 errors + 2301 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 20-Nov-2024 00:07:16 (Found 4 errors + 2303 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 20-Nov-2024 00:07:16 (Found 4 errors + 2304 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 20-Nov-2024 00:07:16 (Found 4 errors + 2306 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 20-Nov-2024 00:07:16 (Found 4 errors + 2309 warnings) Compiling jalview/src/uk/ac/ebi/www build 20-Nov-2024 00:07:16 (Found 4 errors + 2312 warnings) Compiling jalview/src/uk/ac/ebi/www build 20-Nov-2024 00:07:16 (Found 4 errors + 2315 warnings) Compiling jalview/src/uk/ac/ebi/www build 20-Nov-2024 00:07:16 (Found 4 errors + 2322 warnings) Compiling jalview/src/uk/ac/ebi/www build 20-Nov-2024 00:07:16 (Found 4 errors + 2370 warnings) Compiling jalview/src/uk/ac/ebi/www build 20-Nov-2024 00:07:16 (Found 4 errors + 2412 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 20-Nov-2024 00:07:16 (Found 4 errors + 2419 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 20-Nov-2024 00:07:16 (Found 4 errors + 2419 warnings) Compiling jalview/src/vamsas build 20-Nov-2024 00:07:16 (Found 4 errors + 2420 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2422 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2423 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2425 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2426 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2428 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2429 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2431 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2432 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2434 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2435 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2437 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2438 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2440 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2441 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2443 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2444 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2445 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2447 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2449 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2450 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2452 warnings) Compiling jalview/src/vamsas/objects/simple build 20-Nov-2024 00:07:16 (Found 4 errors + 2452 warnings) Cleaning output folder for jalview build 20-Nov-2024 00:07:16 (Found 4 errors + 2452 warnings) Copying resources to the output folder build 20-Nov-2024 00:07:18 (Found 4 errors + 2452 warnings) Analyzing sources build 20-Nov-2024 00:07:18 J2S buildStarting 291 files, contexts.size() = 2, isBatch=true build 20-Nov-2024 00:07:18 (Found 4 errors + 2452 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2460 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2462 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2475 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2488 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2489 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2491 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2532 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2534 warnings) Compiling jalview/test/jalview/analysis build 20-Nov-2024 00:07:20 (Found 4 errors + 2534 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 20-Nov-2024 00:07:20 (Found 4 errors + 2539 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 20-Nov-2024 00:07:20 (Found 4 errors + 2540 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 20-Nov-2024 00:07:20 (Found 4 errors + 2546 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 20-Nov-2024 00:07:20 (Found 4 errors + 2547 warnings) Compiling jalview/test/jalview/bin build 20-Nov-2024 00:07:20 (Found 4 errors + 2548 warnings) Compiling jalview/test/jalview/bin build 20-Nov-2024 00:07:20 (Found 4 errors + 2549 warnings) Compiling jalview/test/jalview/bin build 20-Nov-2024 00:07:20 (Found 4 errors + 2552 warnings) Compiling jalview/test/jalview/bin/argparser build 20-Nov-2024 00:07:20 (Found 4 errors + 2559 warnings) Compiling jalview/test/jalview/commands build 20-Nov-2024 00:07:20 (Found 4 errors + 2560 warnings) Compiling jalview/test/jalview/controller build 20-Nov-2024 00:07:20 (Found 4 errors + 2560 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2561 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2574 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2575 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2577 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2586 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2587 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2589 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2590 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2592 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2593 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2594 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2597 warnings) Compiling jalview/test/jalview/datamodel build 20-Nov-2024 00:07:20 (Found 4 errors + 2598 warnings) Compiling jalview/test/jalview/datamodel/features build 20-Nov-2024 00:07:20 (Found 4 errors + 2599 warnings) Compiling jalview/test/jalview/datamodel/features build 20-Nov-2024 00:07:20 (Found 4 errors + 2599 warnings) Compiling jalview/test/jalview/ext/android build 20-Nov-2024 00:07:20 (Found 4 errors + 2599 warnings) Compiling jalview/test/jalview/ext/ensembl build 20-Nov-2024 00:07:20 (Found 4 errors + 2599 warnings) Compiling jalview/test/jalview/ext/htsjdk build 20-Nov-2024 00:07:20 (Found 4 errors + 2600 warnings) Compiling jalview/test/jalview/ext/jmol build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/ext/jmol build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/ext/paradise build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/ext/pymol build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/ext/rbvi/chimera build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/ext/so build 20-Nov-2024 00:07:20 (Found 4 errors + 2601 warnings) Compiling jalview/test/jalview/fts/core build 20-Nov-2024 00:07:20 (Found 4 errors + 2602 warnings) Compiling jalview/test/jalview/fts/service/pdb build 20-Nov-2024 00:07:20 (Found 4 errors + 2603 warnings) Compiling jalview/test/jalview/fts/service/pdb build 20-Nov-2024 00:07:20 (Found 4 errors + 2610 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 20-Nov-2024 00:07:20 (Found 4 errors + 2615 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 20-Nov-2024 00:07:20 (Found 4 errors + 2615 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:20 (Found 4 errors + 2617 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2619 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2620 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2640 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2665 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2666 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2669 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2670 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2672 warnings) Compiling jalview/test/jalview/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2678 warnings) Compiling jalview/test/jalview/gui/structurechooser build 20-Nov-2024 00:07:21 (Found 4 errors + 2679 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2680 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2684 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2688 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2690 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2691 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2697 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2699 warnings) Compiling jalview/test/jalview/io build 20-Nov-2024 00:07:21 (Found 4 errors + 2699 warnings) Compiling jalview/test/jalview/io/cache build 20-Nov-2024 00:07:21 (Found 4 errors + 2699 warnings) Compiling jalview/test/jalview/io/gff build 20-Nov-2024 00:07:21 (Found 4 errors + 2700 warnings) Compiling jalview/test/jalview/io/gff build 20-Nov-2024 00:07:21 (Found 4 errors + 2709 warnings) Compiling jalview/test/jalview/io/vcf build 20-Nov-2024 00:07:21 (Found 4 errors + 2709 warnings) Compiling jalview/test/jalview/math build 20-Nov-2024 00:07:21 (Found 4 errors + 2713 warnings) Compiling jalview/test/jalview/project build 20-Nov-2024 00:07:21 (Found 4 errors + 2714 warnings) Compiling jalview/test/jalview/renderer build 20-Nov-2024 00:07:21 (Found 4 errors + 2721 warnings) Compiling jalview/test/jalview/renderer build 20-Nov-2024 00:07:21 (Found 4 errors + 2721 warnings) Compiling jalview/test/jalview/renderer/seqfeatures build 20-Nov-2024 00:07:21 (Found 4 errors + 2721 warnings) Compiling jalview/test/jalview/schemes build 20-Nov-2024 00:07:21 (Found 4 errors + 2721 warnings) Compiling jalview/test/jalview/structure build 20-Nov-2024 00:07:21 (Found 4 errors + 2723 warnings) Compiling jalview/test/jalview/structure build 20-Nov-2024 00:07:21 (Found 4 errors + 2724 warnings) Compiling jalview/test/jalview/structure build 20-Nov-2024 00:07:21 (Found 4 errors + 2725 warnings) Compiling jalview/test/jalview/structure build 20-Nov-2024 00:07:21 (Found 4 errors + 2728 warnings) Compiling jalview/test/jalview/structure build 20-Nov-2024 00:07:21 (Found 4 errors + 2728 warnings) Compiling jalview/test/jalview/structures/models build 20-Nov-2024 00:07:21 (Found 4 errors + 2729 warnings) Compiling jalview/test/jalview/urls build 20-Nov-2024 00:07:21 (Found 4 errors + 2734 warnings) Compiling jalview/test/jalview/urls build 20-Nov-2024 00:07:21 (Found 4 errors + 2739 warnings) Compiling jalview/test/jalview/urls build 20-Nov-2024 00:07:21 (Found 4 errors + 2739 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2746 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2747 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2751 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2752 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2757 warnings) Compiling jalview/test/jalview/util build 20-Nov-2024 00:07:21 (Found 4 errors + 2757 warnings) Compiling jalview/test/jalview/util/dialogrunner build 20-Nov-2024 00:07:21 (Found 4 errors + 2757 warnings) Compiling jalview/test/jalview/util/imagemaker build 20-Nov-2024 00:07:21 (Found 4 errors + 2757 warnings) Compiling jalview/test/jalview/util/matcher build 20-Nov-2024 00:07:21 (Found 4 errors + 2760 warnings) Compiling jalview/test/jalview/util/matcher build 20-Nov-2024 00:07:21 (Found 4 errors + 2760 warnings) Compiling jalview/test/jalview/viewmodel build 20-Nov-2024 00:07:21 (Found 4 errors + 2761 warnings) Compiling jalview/test/jalview/viewmodel/styles build 20-Nov-2024 00:07:21 (Found 4 errors + 2761 warnings) Compiling jalview/test/jalview/workers build 20-Nov-2024 00:07:21 (Found 4 errors + 2761 warnings) Compiling jalview/test/jalview/ws build 20-Nov-2024 00:07:21 (Found 4 errors + 2763 warnings) Compiling jalview/test/jalview/ws build 20-Nov-2024 00:07:21 (Found 4 errors + 2766 warnings) Compiling jalview/test/jalview/ws/dbsources build 20-Nov-2024 00:07:21 (Found 4 errors + 2767 warnings) Compiling jalview/test/jalview/ws/dbsources build 20-Nov-2024 00:07:21 (Found 4 errors + 2767 warnings) Compiling jalview/test/jalview/ws/ebi build 20-Nov-2024 00:07:21 (Found 4 errors + 2774 warnings) Compiling jalview/test/jalview/ws/gui build 20-Nov-2024 00:07:21 (Found 4 errors + 2774 warnings) Compiling jalview/test/jalview/ws/jabaws build 20-Nov-2024 00:07:21 (Found 4 errors + 2775 warnings) Compiling jalview/test/jalview/ws/jabaws build 20-Nov-2024 00:07:21 (Found 4 errors + 2776 warnings) Compiling jalview/test/jalview/ws/jabaws build 20-Nov-2024 00:07:21 (Found 4 errors + 2780 warnings) Compiling jalview/test/jalview/ws/jabaws build 20-Nov-2024 00:07:21 (Found 4 errors + 2795 warnings) Compiling jalview/test/jalview/ws/jws2 build 20-Nov-2024 00:07:21 (Found 4 errors + 2795 warnings) Compiling jalview/test/jalview/ws/rest build 20-Nov-2024 00:07:21 (Found 4 errors + 2796 warnings) Compiling jalview/test/jalview/ws/rest build 20-Nov-2024 00:07:21 (Found 4 errors + 2796 warnings) Compiling jalview/test/jalview/ws/seqfetcher build 20-Nov-2024 00:07:21 (Found 4 errors + 2797 warnings) Compiling jalview/test/jalview/ws/sifts build 20-Nov-2024 00:07:21 (Found 4 errors + 2799 warnings) Compiling jalview/test/jalview/ws/utils build 20-Nov-2024 00:07:21 (Found 4 errors + 2815 warnings) Compiling jalview/test/junit/extensions build 20-Nov-2024 00:07:21 (Found 4 errors + 2817 warnings) Compiling jalview/test/junit/extensions build 20-Nov-2024 00:07:21 (Found 4 errors + 2817 warnings) Compiling jalview/test/mc_view build 20-Nov-2024 00:07:21 (Found 4 errors + 2818 warnings) Compiling jalview/test/mc_view build 20-Nov-2024 00:07:21 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/.j2s build 20-Nov-2024 00:07:21 j2s.config.altfileproperty = org.jalview.jalviewjsj2sfilename build 20-Nov-2024 00:07:21 J2S System.getProperty("org.jalview.jalviewjsj2sfilename") = ./build/jalviewjs/config/j2s build 20-Nov-2024 00:07:21 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/./build/jalviewjs/config/j2s build 20-Nov-2024 00:07:21 j2s.compiler.status = enable build 20-Nov-2024 00:07:21 j2s.compiler.java.version = 8 build 20-Nov-2024 00:07:21 J2S compiler version set to 8 build 20-Nov-2024 00:07:21 j2s.break.on.error = false build 20-Nov-2024 00:07:21 j2s.exact.long = true build 20-Nov-2024 00:07:21 j2s.async.thread = false build 20-Nov-2024 00:07:21 j2s.compiler.mode = nodebug build 20-Nov-2024 00:07:21 j2s.site.directory = ./build/jalviewjs/tmp/site_js build 20-Nov-2024 00:07:21 J2S writing to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s build 20-Nov-2024 00:07:21 j2s.log.methods.declared = build 20-Nov-2024 00:07:21 j2s.log.methods.called = build 20-Nov-2024 00:07:21 j2s.excluded.paths = test;testng;util build 20-Nov-2024 00:07:21 j2s.compiler.read.annotations = true build 20-Nov-2024 00:07:21 j2s.compiler.ignored.annotations = CallerSensitive;ConstructorProperties;Deprecated;Override;SafeVarargs;SuppressWarnings;FunctionalInterface;Documented;Inherited;Native;Repeatable;Retention; build 20-Nov-2024 00:07:21 j2s.testing = false build 20-Nov-2024 00:07:21 j2s.compiler.nonqualified.packages = build 20-Nov-2024 00:07:21 j2s.compiler.nonqualified.classes = build 20-Nov-2024 00:07:21 j2s.class.replacements = build 20-Nov-2024 00:07:21 j2s.template.html = utils/jalviewjs/template.html build 20-Nov-2024 00:07:21 J2S using HTML template /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/utils/jalviewjs/template.html build 20-Nov-2024 00:07:21 J2S building JavaScript jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Wed Nov 20 00:07:21 GMT 2024 build 20-Nov-2024 00:07:21 J2S building JavaScript for 1103 files build 20-Nov-2024 00:07:21 J2S transpiling (1/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/github/reinert/jjschema/Attributes.java build 20-Nov-2024 00:07:22 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/com build 20-Nov-2024 00:07:22 J2S transpiling (2/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/AmpersandRule.java build 20-Nov-2024 00:07:22 J2S transpiling (3/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Any.java build 20-Nov-2024 00:07:22 J2S transpiling (4/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/BackG.java build 20-Nov-2024 00:07:22 J2S transpiling (5/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/BackMatch.java build 20-Nov-2024 00:07:22 J2S transpiling (6/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/BackRefRule.java build 20-Nov-2024 00:07:22 J2S transpiling (7/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Backup.java build 20-Nov-2024 00:07:22 J2S transpiling (8/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/BasicStringBufferLike.java build 20-Nov-2024 00:07:22 J2S transpiling (9/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Bits.java build 20-Nov-2024 00:07:22 J2S transpiling (10/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Boundary.java build 20-Nov-2024 00:07:22 J2S transpiling (11/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Bracket.java build 20-Nov-2024 00:07:22 J2S transpiling (12/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/CaseMgr.java build 20-Nov-2024 00:07:22 J2S transpiling (13/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/ChangeRule.java build 20-Nov-2024 00:07:23 J2S transpiling (14/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/CodeRule.java build 20-Nov-2024 00:07:23 J2S transpiling (15/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Ctrl.java build 20-Nov-2024 00:07:23 J2S transpiling (16/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Custom.java build 20-Nov-2024 00:07:23 J2S transpiling (17/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/CustomEndpoint.java build 20-Nov-2024 00:07:23 J2S transpiling (18/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/DirFileRegex.java build 20-Nov-2024 00:07:23 J2S transpiling (19/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/DotMulti.java build 20-Nov-2024 00:07:23 J2S transpiling (20/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/End.java build 20-Nov-2024 00:07:23 J2S transpiling (21/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/FastBracket.java build 20-Nov-2024 00:07:23 J2S transpiling (22/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/FastMulti.java build 20-Nov-2024 00:07:23 J2S transpiling (23/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/FileRegex.java build 20-Nov-2024 00:07:23 J2S transpiling (24/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Group.java build 20-Nov-2024 00:07:23 J2S transpiling (25/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/LeftRule.java build 20-Nov-2024 00:07:23 J2S transpiling (26/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Multi.java build 20-Nov-2024 00:07:23 J2S transpiling (27/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/MultiMin.java build 20-Nov-2024 00:07:23 J2S transpiling (28/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Multi_stage2.java build 20-Nov-2024 00:07:23 J2S transpiling (29/1103) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RegSyntax.java build 20-Nov-2024 00:07:23 J2S transpiling (48/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RegSyntaxError.java build 20-Nov-2024 00:07:23 J2S transpiling (49/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Regex.java build 20-Nov-2024 00:07:23 J2S transpiling (50/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RegexReader.java build 20-Nov-2024 00:07:23 J2S transpiling (51/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RegexTokenizer.java build 20-Nov-2024 00:07:23 J2S transpiling (52/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RegexWriter.java build 20-Nov-2024 00:07:23 >>>main found for com.stevesoft.pat.RegexWriter build 20-Nov-2024 00:07:23 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/./build/jalviewjs/tmp/site_js/com_stevesoft_pat_RegexWriter.html build 20-Nov-2024 00:07:23 J2S transpiling (53/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/ReplaceRule.java build 20-Nov-2024 00:07:24 J2S transpiling (54/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Replacer.java build 20-Nov-2024 00:07:24 J2S transpiling (55/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RightRule.java build 20-Nov-2024 00:07:24 J2S transpiling (56/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Rthings.java build 20-Nov-2024 00:07:24 J2S transpiling (57/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/RuleHolder.java build 20-Nov-2024 00:07:24 J2S transpiling (58/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Skip.java build 20-Nov-2024 00:07:24 J2S transpiling (59/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Skip2.java build 20-Nov-2024 00:07:24 J2S transpiling (60/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/SkipBMH.java build 20-Nov-2024 00:07:24 J2S transpiling (61/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Skipped.java build 20-Nov-2024 00:07:24 J2S transpiling (62/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/SpecialRule.java build 20-Nov-2024 00:07:24 J2S transpiling (63/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Start.java build 20-Nov-2024 00:07:24 J2S transpiling (64/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/StrPos.java build 20-Nov-2024 00:07:24 J2S transpiling (65/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/StringBufferLike.java build 20-Nov-2024 00:07:24 J2S transpiling (66/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/StringLike.java build 20-Nov-2024 00:07:24 J2S transpiling (67/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/StringRule.java build 20-Nov-2024 00:07:24 J2S transpiling (68/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/SubMark.java build 20-Nov-2024 00:07:24 J2S transpiling (69/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/TransPat.java build 20-Nov-2024 00:07:24 J2S transpiling (70/1103) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/src/com/stevesoft/pat/Transformer.java build 20-Nov-2024 00:07:24 J2S transpiling (71/1103) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/util/imagemaker/BitmapImageSizeTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/util/matcher/ConditionTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/util/matcher/MatcherTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/viewmodel/ViewportRangesTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/viewmodel/styles/ViewStyleTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/workers/AlignCalcManagerTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/PDBSequenceFetcherTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/SequenceFetcherTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/EBIAlphaFoldTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/EmblXmlSourceTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/PfamFullTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/PfamSeedTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/RemoteFormatTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/RfamFullTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/RfamSeedTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/UniprotTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/dbsources/XfamFetcherTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/ebi/EBIFetchClientTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/gui/Jws2ParamView.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/jabaws/DisorderAnnotExportImport.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/jabaws/MinJabawsClientTests.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/jabaws/RNAStructExportImport.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/jws2/ParameterUtilsTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/rest/RestClientTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/rest/ShmmrRSBSService.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/seqfetcher/DbRefFetcherTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/sifts/SiftsClientTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/jalview/ws/utils/UrlDownloadClientTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/junit/extensions/PA.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/junit/extensions/PrivilegedAccessor.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/mc_view/AtomTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/mc_view/BondTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/mc_view/PDBChainTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/mc_view/PDBfileTest.java build 20-Nov-2024 00:07:48 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/test/mc_view/ResidueTest.java build 20-Nov-2024 00:07:48 J2S processed 1103 .java files, created 1134 .js files and 7 .html files, copied 6 resources build 20-Nov-2024 00:07:48 J2S buildFinished 1103 files transpiled for /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 build 20-Nov-2024 00:07:48 J2S buildFinished nerror = 0 Wed Nov 20 00:07:48 GMT 2024 build 20-Nov-2024 00:07:48 (Found 4 errors + 2818 warnings) Build done build 20-Nov-2024 00:07:48 Invoking 'Gradle Project Builder' on '/jalview'. build 20-Nov-2024 00:07:49 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) completed. Took 48.222 secs. build 20-Nov-2024 00:07:49 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:50 build 20-Nov-2024 00:07:50 > Task :jalviewjsCopyTransferSiteJs build 20-Nov-2024 00:07:50 Caching disabled for task ':jalviewjsCopyTransferSiteJs' because: build 20-Nov-2024 00:07:50 Build cache is disabled build 20-Nov-2024 00:07:50 Task ':jalviewjsCopyTransferSiteJs' is not up-to-date because: build 20-Nov-2024 00:07:50 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site has been removed. build 20-Nov-2024 00:07:50 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/com_stevesoft_pat_RegexWriter.html has been removed. build 20-Nov-2024 00:07:50 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_GetdownLauncherUpdate.html has been removed. build 20-Nov-2024 00:07:50 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) completed. Took 0.257 secs. build 20-Nov-2024 00:07:50 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:51 build 20-Nov-2024 00:07:51 > Task :jalviewjsTransferUnzipLib build 20-Nov-2024 00:07:51 Caching disabled for task ':jalviewjsTransferUnzipLib' because: build 20-Nov-2024 00:07:51 Build cache is disabled build 20-Nov-2024 00:07:51 Task ':jalviewjsTransferUnzipLib' is not up-to-date because: build 20-Nov-2024 00:07:51 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_lib has been removed. build 20-Nov-2024 00:07:51 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_AlignmentDemo.html has been removed. build 20-Nov-2024 00:07:51 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_fragseq_FragSeqGUI.html has been removed. build 20-Nov-2024 00:07:51 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) completed. Took 0.921 secs. build 20-Nov-2024 00:07:51 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:52 build 20-Nov-2024 00:07:52 > Task :jalviewjsTransferUnzipSwingJs build 20-Nov-2024 00:07:52 Caching disabled for task ':jalviewjsTransferUnzipSwingJs' because: build 20-Nov-2024 00:07:52 Build cache is disabled build 20-Nov-2024 00:07:52 Task ':jalviewjsTransferUnzipSwingJs' is not up-to-date because: build 20-Nov-2024 00:07:52 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_swingjs has been removed. build 20-Nov-2024 00:07:52 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_swingjs/___j2sflags.htm has been removed. build 20-Nov-2024 00:07:52 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_swingjs/debug.log has been removed. build 20-Nov-2024 00:07:52 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) completed. Took 1.367 secs. build 20-Nov-2024 00:07:52 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:52 build 20-Nov-2024 00:07:52 > Task :jalviewjsTransferUnzipAllLibs build 20-Nov-2024 00:07:52 Skipping task ':jalviewjsTransferUnzipAllLibs' as it has no actions. build 20-Nov-2024 00:07:52 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:07:52 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:53 build 20-Nov-2024 00:07:53 > Task :jalviewjsSyncAllLibs build 20-Nov-2024 00:07:53 Caching disabled for task ':jalviewjsSyncAllLibs' because: build 20-Nov-2024 00:07:53 Build cache is disabled build 20-Nov-2024 00:07:53 Task ':jalviewjsSyncAllLibs' is not up-to-date because: build 20-Nov-2024 00:07:53 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/CDL.js has changed. build 20-Nov-2024 00:07:53 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/Cookie.js has changed. build 20-Nov-2024 00:07:53 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/CookieList.js has changed. build 20-Nov-2024 00:07:53 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 1.24 secs. build 20-Nov-2024 00:07:53 :copyResources (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:53 build 20-Nov-2024 00:07:53 > Task :copyResources UP-TO-DATE build 20-Nov-2024 00:07:53 Caching disabled for task ':copyResources' because: build 20-Nov-2024 00:07:53 Build cache is disabled build 20-Nov-2024 00:07:53 Skipping task ':copyResources' as it is up-to-date. build 20-Nov-2024 00:07:53 :copyResources (Thread[Execution worker for ':',5,main]) completed. Took 0.011 secs. build 20-Nov-2024 00:07:53 :createBuildProperties (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:53 build 20-Nov-2024 00:07:53 > Task :createBuildProperties build 20-Nov-2024 00:07:53 Caching disabled for task ':createBuildProperties' because: build 20-Nov-2024 00:07:53 Build cache is disabled build 20-Nov-2024 00:07:53 Task ':createBuildProperties' is not up-to-date because: build 20-Nov-2024 00:07:53 Value of input property 'comment' has changed for task ':createBuildProperties' build 20-Nov-2024 00:07:53 Value of input property 'properties' has changed for task ':createBuildProperties' build 20-Nov-2024 00:07:53 :createBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.003 secs. build 20-Nov-2024 00:07:53 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:53 build 20-Nov-2024 00:07:53 > Task :jalviewjsSyncBuildProperties build 20-Nov-2024 00:07:53 Caching disabled for task ':jalviewjsSyncBuildProperties' because: build 20-Nov-2024 00:07:53 Build cache is disabled build 20-Nov-2024 00:07:53 Task ':jalviewjsSyncBuildProperties' is not up-to-date because: build 20-Nov-2024 00:07:53 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has been removed. build 20-Nov-2024 00:07:53 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.118 secs. build 20-Nov-2024 00:07:53 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:07:55 build 20-Nov-2024 00:07:55 > Task :jalviewjsBuildAllCores build 20-Nov-2024 00:07:55 Execution optimizations have been disabled for task ':jalviewjsBuildAllCores' to ensure correctness due to the following reasons: build 20-Nov-2024 00:07:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_lib/swingjs/j2s'. Reason: Task ':jalviewjsBuildAllCores' uses this output of task ':jalviewjsTransferUnzipLib' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:07:55 Invalidating VFS because task ':jalviewjsBuildAllCores' failed validation build 20-Nov-2024 00:07:55 Caching disabled for task ':jalviewjsBuildAllCores' because: build 20-Nov-2024 00:07:55 Build cache is disabled build 20-Nov-2024 00:07:55 Task ':jalviewjsBuildAllCores' is not up-to-date because: build 20-Nov-2024 00:07:55 Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. build 20-Nov-2024 00:07:55 Creating core for jalview... build 20-Nov-2024 00:07:55 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js build 20-Nov-2024 00:07:55 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 20-Nov-2024 00:07:55 build 20-Nov-2024 00:07:55 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js' build 20-Nov-2024 00:07:55 build 20-Nov-2024 00:07:55 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 20-Nov-2024 00:07:55 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 20-Nov-2024 00:08:04 -- build 20-Nov-2024 00:08:04 Creating core for jvexamplefile... build 20-Nov-2024 00:08:04 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.js build 20-Nov-2024 00:08:04 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js build 20-Nov-2024 00:08:04 build 20-Nov-2024 00:08:04 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js' build 20-Nov-2024 00:08:04 build 20-Nov-2024 00:08:04 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js build 20-Nov-2024 00:08:04 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 20-Nov-2024 00:08:06 -- build 20-Nov-2024 00:08:06 Creating core for _jalview... build 20-Nov-2024 00:08:06 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js build 20-Nov-2024 00:08:06 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js build 20-Nov-2024 00:08:06 build 20-Nov-2024 00:08:06 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js' build 20-Nov-2024 00:08:06 build 20-Nov-2024 00:08:06 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js build 20-Nov-2024 00:08:06 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 20-Nov-2024 00:08:07 -- build 20-Nov-2024 00:08:07 Creating core for _stevesoft... build 20-Nov-2024 00:08:07 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js build 20-Nov-2024 00:08:07 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js build 20-Nov-2024 00:08:07 build 20-Nov-2024 00:08:07 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js' build 20-Nov-2024 00:08:07 build 20-Nov-2024 00:08:07 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js build 20-Nov-2024 00:08:07 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 20-Nov-2024 00:08:10 -- build 20-Nov-2024 00:08:10 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) completed. Took 16.621 secs. build 20-Nov-2024 00:08:10 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:10 build 20-Nov-2024 00:08:10 > Task :jalviewjsPublishCoreTemplates build 20-Nov-2024 00:08:10 Caching disabled for task ':jalviewjsPublishCoreTemplates' because: build 20-Nov-2024 00:08:10 Build cache is disabled build 20-Nov-2024 00:08:10 Task ':jalviewjsPublishCoreTemplates' is not up-to-date because: build 20-Nov-2024 00:08:10 Output property '$1$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_core/JalviewJS_jalview.html has been removed. build 20-Nov-2024 00:08:10 Output property '$1$2' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_core/JalviewJS_jvexamplefile.html has been removed. build 20-Nov-2024 00:08:10 Output property '$1$3' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/tmp/site_core/JalviewJS__jalview.html has been removed. build 20-Nov-2024 00:08:10 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) completed. Took 0.018 secs. build 20-Nov-2024 00:08:10 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:10 build 20-Nov-2024 00:08:10 > Task :jalviewjsSyncCore build 20-Nov-2024 00:08:10 Caching disabled for task ':jalviewjsSyncCore' because: build 20-Nov-2024 00:08:10 Build cache is disabled build 20-Nov-2024 00:08:10 Task ':jalviewjsSyncCore' is not up-to-date because: build 20-Nov-2024 00:08:10 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/JalviewJS__jalview.html has been removed. build 20-Nov-2024 00:08:10 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/JalviewJS__stevesoft.html has been removed. build 20-Nov-2024 00:08:10 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/JalviewJS_jalview.html has been removed. build 20-Nov-2024 00:08:10 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) completed. Took 0.19 secs. build 20-Nov-2024 00:08:10 :copyChannelResources (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:10 build 20-Nov-2024 00:08:10 > Task :copyChannelResources build 20-Nov-2024 00:08:10 Execution optimizations have been disabled for task ':copyChannelResources' to ensure correctness due to the following reasons: build 20-Nov-2024 00:08:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:08:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/resources/resources_build'. Reason: Task ':jalviewjsSyncBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 20-Nov-2024 00:08:10 Invalidating VFS because task ':copyChannelResources' failed validation build 20-Nov-2024 00:08:10 Caching disabled for task ':copyChannelResources' because: build 20-Nov-2024 00:08:10 Build cache is disabled build 20-Nov-2024 00:08:10 Task ':copyChannelResources' is not up-to-date because: build 20-Nov-2024 00:08:10 Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. build 20-Nov-2024 00:08:10 :copyChannelResources (Thread[Execution worker for ':',5,main]) completed. Took 0.276 secs. build 20-Nov-2024 00:08:10 :buildResources (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:10 build 20-Nov-2024 00:08:10 > Task :buildResources build 20-Nov-2024 00:08:10 Skipping task ':buildResources' as it has no actions. build 20-Nov-2024 00:08:10 :buildResources (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:10 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:11 build 20-Nov-2024 00:08:11 > Task :jalviewjsSyncResources build 20-Nov-2024 00:08:11 Caching disabled for task ':jalviewjsSyncResources' because: build 20-Nov-2024 00:08:11 Build cache is disabled build 20-Nov-2024 00:08:11 Task ':jalviewjsSyncResources' is not up-to-date because: build 20-Nov-2024 00:08:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has changed. build 20-Nov-2024 00:08:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/AmbiguityCodes.dat has been removed. build 20-Nov-2024 00:08:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/j2s/authors.props has been removed. build 20-Nov-2024 00:08:11 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) completed. Took 0.17 secs. build 20-Nov-2024 00:08:11 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :jalviewjsSyncSiteResources build 20-Nov-2024 00:08:12 Caching disabled for task ':jalviewjsSyncSiteResources' because: build 20-Nov-2024 00:08:12 Build cache is disabled build 20-Nov-2024 00:08:12 Task ':jalviewjsSyncSiteResources' is not up-to-date because: build 20-Nov-2024 00:08:12 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_JalviewJS2.html has changed. build 20-Nov-2024 00:08:12 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/applets-nocore.html has been removed. build 20-Nov-2024 00:08:12 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/applets.html has been removed. build 20-Nov-2024 00:08:12 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) completed. Took 1.225 secs. build 20-Nov-2024 00:08:12 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :jalviewjsPrepareSite build 20-Nov-2024 00:08:12 Skipping task ':jalviewjsPrepareSite' as it has no actions. build 20-Nov-2024 00:08:12 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:12 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :jalviewjsBuildSite build 20-Nov-2024 00:08:12 Skipping task ':jalviewjsBuildSite' as it has no actions. build 20-Nov-2024 00:08:12 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:12 :cleanJalviewjsChromiumUserDir (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :cleanJalviewjsChromiumUserDir UP-TO-DATE build 20-Nov-2024 00:08:12 Caching disabled for task ':cleanJalviewjsChromiumUserDir' because: build 20-Nov-2024 00:08:12 Build cache is disabled build 20-Nov-2024 00:08:12 Skipping task ':cleanJalviewjsChromiumUserDir' as it is up-to-date. build 20-Nov-2024 00:08:12 :cleanJalviewjsChromiumUserDir (Thread[Execution worker for ':',5,main]) completed. Took 0.001 secs. build 20-Nov-2024 00:08:12 :jalviewjsChromiumProfile (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :jalviewjsChromiumProfile build 20-Nov-2024 00:08:12 Caching disabled for task ':jalviewjsChromiumProfile' because: build 20-Nov-2024 00:08:12 Build cache is disabled build 20-Nov-2024 00:08:12 Task ':jalviewjsChromiumProfile' is not up-to-date because: build 20-Nov-2024 00:08:12 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/chromium/First Run has been removed. build 20-Nov-2024 00:08:12 :jalviewjsChromiumProfile (Thread[Execution worker for ':',5,main]) completed. Took 0.002 secs. build 20-Nov-2024 00:08:12 :jalviewjsCopyStderrLaunchFile (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 build 20-Nov-2024 00:08:12 > Task :jalviewjsCopyStderrLaunchFile build 20-Nov-2024 00:08:12 Caching disabled for task ':jalviewjsCopyStderrLaunchFile' because: build 20-Nov-2024 00:08:12 Build cache is disabled build 20-Nov-2024 00:08:12 Task ':jalviewjsCopyStderrLaunchFile' is not up-to-date because: build 20-Nov-2024 00:08:12 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html has been removed. build 20-Nov-2024 00:08:12 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html has been removed. build 20-Nov-2024 00:08:12 :jalviewjsCopyStderrLaunchFile (Thread[Execution worker for ':',5,main]) completed. Took 0.09 secs. build 20-Nov-2024 00:08:12 :jalviewjsLaunchTest (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:12 COMMAND: '/home/bamboo/buildtools/chromium/chrome --no-sandbox --headless=new --disable-gpu --timeout=40000 --virtual-time-budget=40000 --user-data-dir=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/chromium --profile-directory=BUILD --allow-file-access-from-files --enable-logging=stderr file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html' build 20-Nov-2024 00:08:12 Starting process 'command '/home/bamboo/buildtools/chromium/chrome''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1 Command: /home/bamboo/buildtools/chromium/chrome --no-sandbox --headless=new --disable-gpu --timeout=40000 --virtual-time-budget=40000 --user-data-dir=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/chromium --profile-directory=BUILD --allow-file-access-from-files --enable-logging=stderr file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html build 20-Nov-2024 00:08:12 Successfully started process 'command '/home/bamboo/buildtools/chromium/chrome'' build 20-Nov-2024 00:08:14 build 20-Nov-2024 00:08:14 > Task :jalviewjsLaunchTest build 20-Nov-2024 00:08:14 Caching disabled for task ':jalviewjsLaunchTest' because: build 20-Nov-2024 00:08:14 Build cache is disabled build 20-Nov-2024 00:08:14 Task ':jalviewjsLaunchTest' is not up-to-date because: build 20-Nov-2024 00:08:14 Task has not declared any outputs despite executing actions. build 20-Nov-2024 00:08:15 error 20-Nov-2024 00:08:15 [10142:10142:1120/000815.452557:WARNING:chrome_main_delegate.cc(593)] This is Thorium version: 114.0.5735.134 (not a warning) error 20-Nov-2024 00:08:16 [10142:10142:1120/000816.006784:WARNING:chrome_browser_cloud_management_controller.cc(87)] Could not create policy manager as CBCM is not enabled. error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.246003:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.252609:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.252629:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.252642:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:17 [10142:10142:1120/000817.537626:ERROR:chrome_browser_cloud_management_controller.cc(162)] Cloud management controller initialization aborted as CBCM is not enabled. error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.771938:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:17 [10142:10160:1120/000817.771963:ERROR:bus.cc(399)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix") error 20-Nov-2024 00:08:18 [10173:10173:1120/000818.079559:ERROR:vaapi_wrapper.cc(3273)] Failed to initialize VAAPI libs error 20-Nov-2024 00:08:18 [10173:10173:1120/000818.103143:WARNING:sandbox_linux.cc(393)] InitializeSandbox() called with multiple threads in process gpu-process. error 20-Nov-2024 00:08:18 [10142:10157:1120/000818.156343:WARNING:external_pref_loader.cc(294)] You are using an old-style extension deployment method (external_extensions.json), which will soon be deprecated. (see http://developer.chrome.com/extensions/external_extensions.html) error 20-Nov-2024 00:08:18 [10175:10204:1120/000818.245382:WARNING:dns_client.cc(268)] BuildEffectiveConfig(): invalid configuration error 20-Nov-2024 00:08:18 [10175:10204:1120/000818.246770:WARNING:dns_client.cc(268)] BuildEffectiveConfig(): invalid configuration error 20-Nov-2024 00:08:19 [10142:10142:1120/000818.970271:WARNING:bluez_dbus_manager.cc(247)] Floss manager not present, cannot set Floss enable/disable. error 20-Nov-2024 00:08:19 [10142:10142:1120/000818.970388:ERROR:object_proxy.cc(590)] Failed to call method: org.freedesktop.portal.Settings.Read: object_path= /org/freedesktop/portal/desktop: unknown error type: error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.696005:INFO:CONSOLE(13141)] "J2SApplet load testApplet loadClazz...", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (13141) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.696037:INFO:CONSOLE(13141)] "J2SApplet load testApplet start applet...", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (13141) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.764518:INFO:CONSOLE(13084)] "j2sApplet exec testApplet loadClazz null -- OK", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (13084) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.783705:INFO:CONSOLE(16968)] "j2sApplet exec testApplet start applet null error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.783728:INFO:CONSOLE(13084)] "j2sApplet exec testApplet start applet null -- OK", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (13084) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.786561:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Class.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.794967:INFO:CONSOLE(26)] "transpiler was unknown now 3.3.1-v1 for java.lang.Class error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.794989:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/Jalview.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.798288:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/groovy/JalviewObjectI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.800673:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/Platform.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.803195:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/Console.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.805979:INFO:CONSOLE(16968)] "Platform adding known access-control-allow-origin * for domain https://www.jalview.org error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.806000:INFO:CONSOLE(16968)] "Platform adding known access-control-allow-origin * for domain http://www.jalview.org error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.806013:INFO:CONSOLE(16968)] "Platform adding known access-control-allow-origin * for domain http://www.compbio.dundee.ac.uk error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.806023:INFO:CONSOLE(16968)] "Platform adding known access-control-allow-origin * for domain https://www.compbio.dundee.ac.uk error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.806167:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Hashtable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.813422:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Dictionary.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.816448:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Map.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.819973:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/HashMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.826289:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.830686:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSAppletViewer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.834318:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSFrameViewer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.838092:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSApp.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.840133:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/js/JSInterface.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.842347:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/applet/AppletStub.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.844008:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/applet/AppletContext.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.846203:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/URL.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.848895:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/Interface.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.851133:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of javajs.util.AjaxURLStreamHandlerFactory error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.851158:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/AjaxURLStreamHandlerFactory.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.856814:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/URLStreamHandlerFactory.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.859530:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractSet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.862526:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractCollection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.867152:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Collection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.870382:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Iterable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.873940:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Set.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.882155:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Enumeration.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.885078:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Iterator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.889241:INFO:CONSOLE(16968)] "JSApp get parameter: language = null error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.889270:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSUtil.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.894063:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/JSUtilI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.896432:INFO:CONSOLE(16968)] "swingjs.JSUtil initialized;debug=false error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.896456:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Locale.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.900951:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/BaseLocale.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.904949:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/StringBuilder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.907253:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/AbstractStringBuilder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.911123:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/LocaleUtils.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.914838:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Enum.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.916331:INFO:CONSOLE(16968)] "JSApp get parameter: name = testApplet error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.916362:INFO:CONSOLE(16968)] "JSApp get parameter: syncId = 692286210062364 error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.916387:INFO:CONSOLE(16968)] "JSApp initialized error 20-Nov-2024 00:08:19 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:19 [10142:10142:1120/000819.916402:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Dimension.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.936231:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/geom/Dimension2D.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.939395:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/Lst.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.942703:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/ArrayList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.945616:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.948577:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/List.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.950841:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/RandomAccess.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.954431:INFO:CONSOLE(16968)] "JSAppletViewer initializing2 error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.954457:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Insets.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.957697:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSThreadGroup.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.959784:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/ThreadGroup.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.961984:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Thread.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.966674:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/JSThread.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.974113:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSAppletThread.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.978372:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/SunToolkit.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.981459:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Toolkit.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.984984:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/ComponentFactory.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.986684:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/EventQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000819.989491:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Queue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.001832:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/AppContext.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.004641:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/PostEventQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.008207:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSToolkit.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.014044:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/beans/PropertyChangeSupport.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.021052:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/beans/ChangeListenerMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.023588:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/beans/PropertyChangeListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.027433:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/EventListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.032362:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/MostRecentThreadAppContext.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.036353:INFO:CONSOLE(16968)] "JSToolkit initialized error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.036373:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSGraphicsConfiguration.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.038976:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/GraphicsConfiguration.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.041151:INFO:CONSOLE(16968)] "JSGraphicsConfiguration initialized error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.041171:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/GraphicsEnvironment.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.043214:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of swingjs.JSGraphicsEnvironment error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.043233:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSGraphicsEnvironment.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.045342:INFO:CONSOLE(16968)] "JSGraphicsEnvironment initialized error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.045360:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of swingjs.JSScreenDevice error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.045374:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSScreenDevice.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.047403:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/GraphicsDevice.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.049537:INFO:CONSOLE(16968)] "JSScreenDevice initialized error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.057687:INFO:CONSOLE(16968)] "JSAppletViewer thread run1 mode=0 status=0 error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.057709:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SwingUtilities.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.062219:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SwingConstants.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.065664:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/MostRecentKeyValue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.069332:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/InvocationEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.077081:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/AWTEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.079686:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/EventObject.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.084178:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/ActiveEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.086789:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/AWTAutoShutdown.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.090175:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/HashSet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.092322:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/IdentityHashMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.095341:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/EventDispatchThread.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.098504:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/EventQueueItem.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.101417:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/EventFilter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.105449:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Arrays.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.110684:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/LinkedHashMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.114821:INFO:CONSOLE(16968)] "JSAppletViewer thread run1 mode=1 status=1 error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.114841:INFO:CONSOLE(16968)] "JSAppletViewer runloader error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.114869:INFO:CONSOLE(16968)] "JSApp get parameter: main = jalview.bin.Jalview error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.114881:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of swingjs.JSDummyApplet error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.115409:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSDummyApplet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.118064:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JApplet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.126647:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/applet/JSApplet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.128635:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/JSPanel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.130548:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Container.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.133456:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/JSComponent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.135642:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Component.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.141345:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/image/ImageObserver.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.144411:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/RootPaneContainer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.147258:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/FlowLayout.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.148865:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/LayoutManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.151056:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/ComponentOrientation.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.153971:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JRootPane.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.157828:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JComponent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.163693:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/RequestFocusController.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.166060:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/EventListenerList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.168399:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JPanel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.170776:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/UIManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.173296:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of swingjs.plaf.HTML5LookAndFeel error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.173368:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/HTML5LookAndFeel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.175270:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/LookAndFeel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.178540:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/FontUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.179843:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Font.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.183727:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/UIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.188971:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/UIDefaults.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.193042:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Color.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.195783:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Paint.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.197420:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Transparency.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.199819:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/ColorUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.202938:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/swing/SwingLazyValue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.206000:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/InsetsUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.207940:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/BorderUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.213506:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/Border.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.216522:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/EtchedBorder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.218958:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/AbstractBorder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.223246:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/DimensionUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.226240:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/EmptyBorder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.230598:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/RepaintManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.235906:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SwingPaintEventDispatcher.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.237576:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/PaintEventDispatcher.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.239275:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSPanelUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.244305:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSLightweightUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.246002:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSComponentUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.249514:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/ComponentUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.251424:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/peer/ComponentPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.253033:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSEventHandler.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.254764:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/ChangeListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.256392:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/dnd/peer/DropTargetPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.258155:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/peer/LightweightPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.259748:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/peer/ContainerPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.263219:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/beans/PropertyChangeEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.265117:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/KeyboardFocusManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.268327:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/KeyEventDispatcher.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.271122:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/KeyEventPostProcessor.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.272828:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/AWTKeyStroke.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.276187:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/LinkedList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.278902:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractSequentialList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.280815:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Deque.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.282702:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Queue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.285472:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/DefaultKeyboardFocusManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.287947:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/DefaultFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.290134:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/ContainerOrderFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.292588:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/FocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.295342:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Collections.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.303222:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSFocusPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.304127:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/peer/KeyboardFocusManagerPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.306309:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/js/DOMNode.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.309923:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Cursor.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.314027:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JLayeredPane.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.316956:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSLayeredPaneUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.320726:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/BorderLayout.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.322759:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/LayoutManager2.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.324831:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/ArrayTable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.327345:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/FocusManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.329142:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/LayoutFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.330956:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SortingFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.333134:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/InternalFrameFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.335948:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SwingContainerOrderFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.337919:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SwingDefaultFocusTraversalPolicy.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.339669:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/LayoutComparator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.341609:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Comparator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.346796:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSRootPaneUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.350593:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSAppletUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.355175:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/LightweightDispatcher.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.362067:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/AWTEventListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.363660:INFO:CONSOLE(16968)] "testApplet loaded error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.364151:INFO:CONSOLE(298)] "testApplet loaded", source: swingjs/j2s/swingjs/JSUtil.js (298) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.393885:INFO:CONSOLE(16968)] "JSAppletViewer thread run1 mode=1 status=76 error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.393914:INFO:CONSOLE(16968)] "testApplet running jalview.bin.Jalview error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.393928:INFO:CONSOLE(298)] "testApplet running jalview.bin.Jalview", source: swingjs/j2s/swingjs/JSUtil.js (298) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.394395:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/PT.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.398541:INFO:CONSOLE(16968)] "Running main(args) in class jalview.bin.Jalview error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.403709:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/argparser/BootstrapArgs.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.406019:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Objects.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.408118:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/argparser/Arg.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.411468:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/ChannelProperties.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.413710:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Properties.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.416876:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/File.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.418978:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/FileSystem.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.421070:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/AjaxURLStreamHandler.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.422916:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/URLStreamHandler.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.425505:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/channel.props", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.510425:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/BufferedInputStream.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.512415:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/FilterInputStream.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.515051:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/InputStream.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.516739:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/Closeable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.518329:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/AutoCloseable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.520049:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/ByteArrayInputStream.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.524173:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/HttpUtils.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.526366:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/AjaxURLConnection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.528959:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/HttpURLConnection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.530906:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/URLConnection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.532945:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/net/ContentHandler.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.535416:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/Rdr.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.537424:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/api/GenericLineReader.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.540163:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/AU.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.545191:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/jalview_test-release_logo-16.png", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.547200:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/ImageIcon.js", source: 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[10142:10142:1120/000820.584021:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/image/DirectColorModel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.586432:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/image/PackedColorModel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.588560:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/color/ColorSpace.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.591020:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/image/Raster.js", source: 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[10142:10142:1120/000820.600381:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/image/SunWritableRaster.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.602654:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/image/WritableRaster.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.604426:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/java2d/StateTrackable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.606800:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/java2d/StateTrackableDelegate.js", source: 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[10142:10142:1120/000820.653875:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javajs/util/Base64.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.658381:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/jalview_test-release_logo-32.png", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.664274:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/jalview_test-release_logo-48.png", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.677685:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/jalview_test-release_logo-64.png", 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[10142:10142:1120/000820.713276:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/DateFormat.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.715297:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/Format.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.717410:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/DateFormatProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.719297:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/spi/LocaleServiceProvider.js", source: 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20-Nov-2024 00:08:20 [10142:10142:1120/000820.741395:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/AuxLocaleProviderAdapter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.745139:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/LocaleDataMetaInfo.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.746922:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/StringTokenizer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.749885:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/security/PrivilegedAction.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.751225:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/security/AccessController.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.753998:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/DateFormatProviderImpl.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.755491:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/AvailableLanguageTags.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.757471:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/LanguageTag.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.760338:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/SimpleDateFormat.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.763210:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/AttributedCharacterIterator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.765324:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/CharacterIterator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.773320:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/TimeZone.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.809003:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/ZoneInfo.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.811257:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/ZoneInfoFile.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.814487:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/sun/util/calendar/tzdb.dat", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.822743:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/DataInputStream.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.824573:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/io/DataInput.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.838017:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Calendar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.841433:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/spi/CalendarProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.843720:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/CalendarProviderImpl.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.845877:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/GregorianCalendar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.849053:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/CalendarSystem.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.850669:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of sun.util.calendar.Gregorian error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.850813:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/Gregorian.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.855536:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/BaseCalendar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.856623:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/AbstractCalendar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.859286:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/CalendarDataUtility.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.861275:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/spi/CalendarDataProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.863023:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/LocaleServiceProviderPool.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.866258:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/BreakIteratorProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.867871:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/CollatorProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.869608:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/DateFormatSymbolsProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.871121:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/DecimalFormatSymbolsProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.873037:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/spi/NumberFormatProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.874875:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/spi/CurrencyNameProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.876619:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/spi/LocaleNameProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.878229:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/spi/TimeZoneNameProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.880452:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/CalendarDataProviderImpl.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.882369:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/security/PrivilegedExceptionAction.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.884493:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/ServiceLoader.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.887818:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/locale/provider/LocaleResources.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.889953:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/ref/ReferenceQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.891597:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/resources/LocaleData.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.893933:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/ResourceBundle.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.897795:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/CalendarData.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.898235:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/sun/util/resources/CalendarData.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.900427:INFO:CONSOLE(16968)] "JSUtil caching 1780 bytes for swingjs/j2s/sun/util/resources/CalendarData.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.900460:INFO:CONSOLE(16968)] "swingjs.api.Interface creating instance of java.util.PropertyResourceBundle error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.900588:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/PropertyResourceBundle.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.907037:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/en/CalendarData_en.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.907065:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/sun/util/resources/en/CalendarData_en.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.909931:INFO:CONSOLE(16968)] "JSUtil caching 1943 bytes for swingjs/j2s/sun/util/resources/en/CalendarData_en.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.909954:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/en/CalendarData_en_GB.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.909968:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/sun/util/resources/en/CalendarData_en_GB.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.913515:INFO:CONSOLE(16968)] "JSUtil caching 1786 bytes for swingjs/j2s/sun/util/resources/en/CalendarData_en_GB.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.913535:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/CalendarData.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.913548:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/en/CalendarData_en.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.913558:INFO:CONSOLE(16968)] "JSUtil getting Java resource sun/util/resources/en/CalendarData_en_GB.properties error 20-Nov-2024 00:08:20 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:20 [10142:10142:1120/000820.913570:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/CalendarDate.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.917922:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/calendar/CalendarUtils.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.919650:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/DateFormatSymbols.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.921917:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/text/resources/FormatData.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.924681:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/util/resources/ParallelListResourceBundle.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.927683:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/text/resources/en/FormatData_en.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.929824:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/text/resources/en/FormatData_en_GB.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.932569:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/NumberFormat.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.935205:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/DecimalFormatSymbols.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.938734:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/DecimalFormat.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.943108:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/FieldPosition.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.945370:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/text/DigitList.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.947339:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/math/RoundingMode.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.954289:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/LaunchUtils.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.956382:INFO:CONSOLE(16968)] "Jalview Test Version: TEST error 20-Nov-2024 00:08:21 Jalview Test Installation: unknown error 20-Nov-2024 00:08:21 Channel: test-release error 20-Nov-2024 00:08:21 Build Date: unknown error 20-Nov-2024 00:08:21 Preferences file: unknown error 20-Nov-2024 00:08:21 Log file: unknown error 20-Nov-2024 00:08:21 Java version: 1.8 error 20-Nov-2024 00:08:21 Java home: https://. error 20-Nov-2024 00:08:21 Java launch class: unknown error 20-Nov-2024 00:08:21 Java platform: Mozilla/5.0 5.0 (X11) (Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/114.0.0.0 Safari/537.36) error 20-Nov-2024 00:08:21 Java LAF: SwingJS (swingjs.plaf.HTML5LookAndFeel) error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.956629:INFO:CONSOLE(26)] "Using default properties file '/TEMP/swingjs/.jalview_test_properties' error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.956772:INFO:CONSOLE(26)] "Falling back to properties file '/TEMP/swingjs/.jalview_properties' error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.956873:INFO:CONSOLE(26)] "Could not load bootstrap preferences file '/TEMP/swingjs/.jalview_properties' error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.957203:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/.build_properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.959277:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/.build_properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.961592:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/BuildDetails.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.963437:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/api/BuildDetailsI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.965329:INFO:CONSOLE(16968)] "Jalview Test version: 2.11.4.1-test (Source git-commit:6d1fc3490c [releases/Release_2_11_4_Branch]) error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.965558:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/ArgsParser.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.969063:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Vector.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.971490:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/log/JLoggerI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.973247:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/log/JLogger.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.975241:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/log/JLoggerLog4j.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.977495:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Runtime.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.979997:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/ApplicationShutdownHooks.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.982249:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/Shutdown.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.987220:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/authors.props", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.989301:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/authors.props", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.992641:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/.build_properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.993833:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/ws/sifts/SiftsSettings.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000820.998328:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/urls/IdOrgSettings.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.000420:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/PIRFile.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.002577:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/AlignFile.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.004964:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/FileParse.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.007249:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/AlignmentFileReaderI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.009176:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/AlignmentFileWriterI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.010708:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/argparser/ArgParser.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.013538:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/EnumSet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.015332:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/JumboEnumSet.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.018874:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/ArgParserUtils.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.022991:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/FileFormats.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.025494:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/FileFormat.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.026781:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/FileFormatI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.032799:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/UserAgent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.034583:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/gui/Desktop.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.038423:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/jbgui/GDesktop.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.040298:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JFrame.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.042362:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/JSFrame.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.044964:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Window.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.049113:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/WindowConstants.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.051527:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/dnd/DropTargetListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.054047:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/datatransfer/ClipboardOwner.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.055699:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/gui/IProgressIndicator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.057346:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/api/StructureSelectionManagerProvider.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.059738:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/gui/SplashScreen.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.062412:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/HyperlinkListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.066645:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/barton_group-32.png", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.071066:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/images/UoD_banner-32.png", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.085960:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSGraphics2D.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.090004:INFO:CONSOLE(16968)] "JSGraphics2D pixelRatio is 1.0 error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.090027:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/RenderingHints.js", source: 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[10142:10142:1120/000821.112407:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSFrameUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.116134:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSWindowUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.118305:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/peer/WindowPeer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.119786:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/WindowListener.js", source: 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[10142:10142:1120/000821.126664:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/ContainerListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.128216:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/FocusListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.129747:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/KeyListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.131703:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/MouseListener.js", source: 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[10142:10142:1120/000821.140593:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/ActionListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.142362:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/ItemListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.145330:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/AdjustmentListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.148985:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/TextListener.js", source: 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[10142:10142:1120/000821.155556:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/MouseWheelListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.159309:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JMenuBar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.161318:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/MenuElement.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.163103:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/DefaultSingleSelectionModel.js", source: 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[10142:10142:1120/000821.170844:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/BoxLayout.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.173198:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/swing/DefaultLookup.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.176219:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/LazyActionMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.180034:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/ActionMapUIResource.js", source: 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[10142:10142:1120/000821.191256:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/AbstractButton.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.194089:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/ItemSelectable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.196432:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/DefaultButtonModel.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.198453:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/ButtonModel.js", source: 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[10142:10142:1120/000821.206795:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/MenuListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.209094:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/basic/BasicBorders.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.211422:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/reflect/Constructor.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.213186:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/reflect/AccessibleObject.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.214882:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/lang/reflect/AnnotatedElement.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.216936:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/ButtonListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.219283:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/AncestorListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.222106:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/plaf/ComponentInputMapUIResource.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.224637:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/ComponentInputMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.226285:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/InputMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.239083:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/BorderFactory.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.241768:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/BevelBorder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.274893:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JCheckBoxMenuItem.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.276662:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JToggleButton.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.279933:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSCheckBoxMenuItemUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.282070:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSCheckBoxUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.283656:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSRadioButtonUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.298964:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/gui/APQHandlers.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.300658:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/MessageManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.302721:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/Formatter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.306181:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/regex/Pattern.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.309548:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/regex/Matcher.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.311930:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/regex/MatchResult.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.319447:INFO:CONSOLE(16968)] "INFO: Getting messages for lang: en_GB error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.319870:INFO:CONSOLE(16968)] "JSUtil getting Java resource lang/Messages.properties error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.320099:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/lang/Messages.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.329710:INFO:CONSOLE(16968)] "JSUtil caching 90933 bytes for swingjs/j2s/lang/Messages.properties error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.349744:INFO:CONSOLE(16968)] "JSUtil getting Java resource lang/Messages_en.properties error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.349767:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/lang/Messages_en.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.354089:INFO:CONSOLE(16968)] "JSUtil getting Java resource lang/Messages_en_GB.properties error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.354108:INFO:CONSOLE(10504)] "xhr.open binary async=false url=swingjs/j2s/lang/Messages_en_GB.properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.359529:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/JSFontMetrics.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.362271:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/FontMetrics.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.364394:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/font/FontRenderContext.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.379030:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/ShortcutKeyMaskExWrapper.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.381046:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/ShortcutKeyMaskExWrapper8.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.382648:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/util/ShortcutKeyMaskExWrapperI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.384501:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/KeyStroke.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.388018:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/KeyEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.389927:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/InputEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.391650:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/ComponentEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.416412:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/ToolTipManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.418455:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/MouseAdapter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.420409:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/Timer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.423081:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/MouseMotionAdapter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.425656:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/ContainerEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.428406:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JPopupMenu.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.431035:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSPopupMenuUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.433135:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/jquery/JQueryUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.438835:INFO:CONSOLE(16968)] "JSUtil getting Java resource swingjs/jquery/j2sMenu.js error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.439128:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/jquery/j2sMenu.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.440731:INFO:CONSOLE(16968)] "Processing swingjs/j2s/swingjs/jquery/j2sMenu.js [24845] error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.442471:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/MenuKeyListener.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.444757:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/WindowAdapter.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.448537:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/border/CompoundBorder.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.453796:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JSeparator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.456285:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSPopupMenuSeparatorUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.457832:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSSeparatorUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.479782:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/KeyboardManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.507097:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/SizeRequirements.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.518588:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/event/ChangeEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.543537:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/gui/JalviewChangeSupport.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.545413:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/Executors.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.547752:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/TimeUnit.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.550419:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/LinkedBlockingQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.552498:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/AbstractQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.554257:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/BlockingQueue.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.556694:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/atomic/AtomicInteger.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.558498:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/locks/ReentrantLock.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.560406:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/locks/Lock.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.562492:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/locks/AbstractQueuedSynchronizer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.564785:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/locks/AbstractOwnableSynchronizer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.566793:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/locks/Condition.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.569557:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/ThreadPoolExecutor.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.572373:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/AbstractExecutorService.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.575077:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/ExecutorService.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.576440:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/Executor.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.578641:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/RejectedExecutionHandler.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.580820:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/ThreadFactory.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.583279:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/concurrent/Semaphore.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.585512:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/structure/StructureSelectionManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.589306:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/JDesktopPane.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.592123:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/JSDesktopPaneUI.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.596579:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/DefaultDesktopManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.599025:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/swing/DesktopManager.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.604703:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/dnd/DropTarget.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.607386:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/dnd/DropTargetContext.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.609276:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/datatransfer/SystemFlavorMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.611493:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/datatransfer/FlavorMap.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.613300:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/datatransfer/FlavorTable.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.616512:INFO:CONSOLE(16968)] "INFO: JALVIEWJS: CREATED DESKTOP error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.616770:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/JalviewTaskbar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.618579:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/Taskbar.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.621468:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/plaf/Resizer.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.624611:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/js/JSFunction.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.643471:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/WindowEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.645503:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/bin/Commands.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.649247:INFO:CONSOLE(16968)] "WARN: Error when running commands error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (16968) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.649453:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/jalview/io/FileLoader.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.703595:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/javax/net/ssl/HttpsURLConnection.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.706433:INFO:CONSOLE(10504)] "xhr.open binary async=false url=https://www.jalview.org/jalview-js//swingjs/j2s/build_properties", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (10504) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.723468:INFO:CONSOLE(26)] "Non-fatal exception when checking version at https://www.jalview.org/jalview-js//swingjs/j2s/build_properties: error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.723606:INFO:CONSOLE(26)] "java.io.FileNotFoundException: opening https://www.jalview.org/jalview-js//swingjs/j2s/build_properties error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.723713:INFO:CONSOLE(26)] "anonymous.anonymous(Unknown Source) error 20-Nov-2024 00:08:21 ", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/jalview_bin_Jalview-stderr.html (26) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.745768:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/swingjs/api/js/HTML5CanvasContext2D.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.748634:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/GraphicsCallback.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.751078:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/SunGraphicsCallback.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.776000:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/CausedFocusEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.779094:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/event/FocusEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.782359:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/TimSort.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.785999:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/util/ListIterator.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.841172:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/java/awt/SentEvent.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:21 [10142:10142:1120/000821.854840:INFO:CONSOLE(9663)] "xhr.open async=false url=swingjs/j2s/sun/awt/EventQueueItem.js", source: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build/jalviewjs/site/swingjs/swingjs2.js (9663) error 20-Nov-2024 00:08:22 [10142:10142:1120/000821.937952:WARNING:pref_notifier_impl.cc(41)] Pref observer for media_router.cast_allow_all_ips found at shutdown. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 > Task :jalviewjsLaunchTest build 20-Nov-2024 00:08:27 Found line '[10142:10142:1120/000821.616512:INFO:CONSOLE(16968)] "INFO: JALVIEWJS: CREATED DESKTOP' build 20-Nov-2024 00:08:27 :jalviewjsLaunchTest (Thread[Execution worker for ':',5,main]) completed. Took 14.634 secs. build 20-Nov-2024 00:08:27 :jalviewjs (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 > Task :jalviewjs build 20-Nov-2024 00:08:27 Skipping task ':jalviewjs' as it has no actions. build 20-Nov-2024 00:08:27 :jalviewjs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:27 producer locations for task group 0 (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:27 producer locations for task group 0 (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:27 producer locations for task group 1 (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:27 producer locations for task group 1 (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:27 producer locations for task group 2 (Thread[Execution worker for ':',5,main]) started. build 20-Nov-2024 00:08:27 producer locations for task group 2 (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 Execution optimizations have been disabled for 2 invalid unit(s) of work during this build to ensure correctness. build 20-Nov-2024 00:08:27 Please consult deprecation warnings for more details. build 20-Nov-2024 00:08:27 build 20-Nov-2024 00:08:27 BUILD SUCCESSFUL in 1m 51s build 20-Nov-2024 00:08:27 27 actionable tasks: 24 executed, 3 up-to-date simple 20-Nov-2024 00:08:27 Finished task 'JalviewJS ${bamboo.CHANNEL} release' with result: Success command 20-Nov-2024 00:08:27 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE simple 20-Nov-2024 00:08:27 Starting task 'Create tar of getdown ${bamboo.CHANNEL} channel website' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 20-Nov-2024 00:08:27 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-4202243983555396046.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_repository_46497969_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GTC0-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=29\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_7=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 --info eclipse jalviewjsCreateJ2sSettings jalviewjs\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GTC0 clean getdown shadowJar\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_8=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=1.8 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 getdown shadowJar\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\n build 20-Nov-2024 00:08:27 11/ build 20-Nov-2024 00:08:27 11/channel_launch-test-release.jvl build 20-Nov-2024 00:08:27 11/install/ build 20-Nov-2024 00:08:27 11/install/build_properties build 20-Nov-2024 00:08:27 11/install/getdown-launcher.jar build 20-Nov-2024 00:08:27 11/install/getdown.txt build 20-Nov-2024 00:08:27 11/digest2.txt build 20-Nov-2024 00:08:27 11/channel.props build 20-Nov-2024 00:08:27 11/getdown-launcher-new.jar build 20-Nov-2024 00:08:27 11/alt/ build 20-Nov-2024 00:08:27 11/alt/Jmol-NO_LOG4J-14.31.53.jar build 20-Nov-2024 00:08:27 11/alt/log4j-core-2.17.1.jar build 20-Nov-2024 00:08:27 11/alt/groovy-ant-4.0.15.jar build 20-Nov-2024 00:08:27 11/alt/apache-mime4j-0.6.jar build 20-Nov-2024 00:08:27 11/alt/groovy-console-4.0.15.jar build 20-Nov-2024 00:08:27 11/alt/axis.jar build 20-Nov-2024 00:08:27 11/alt/groovy-nio-4.0.15.jar build 20-Nov-2024 00:08:27 11/alt/javax.activation-api-1.2.0.jar build 20-Nov-2024 00:08:27 11/alt/jaxb-runtime-2.3.2.jar build 20-Nov-2024 00:08:27 11/alt/groovy-astbuilder-4.0.15.jar build 20-Nov-2024 00:08:27 11/alt/commons-math3-3.6.1.jar build 20-Nov-2024 00:08:28 11/alt/groovy-json-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/httpclient-4.0.3.jar build 20-Nov-2024 00:08:28 11/alt/jaxws-api-2.3.1.jar build 20-Nov-2024 00:08:28 11/alt/saaj-impl.jar build 20-Nov-2024 00:08:28 11/alt/mail-MODULE.jar build 20-Nov-2024 00:08:28 11/alt/groovy-groovydoc-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/httpcore-4.0.1.jar build 20-Nov-2024 00:08:28 11/alt/groovy-test-junit5-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/regex.jar build 20-Nov-2024 00:08:28 11/alt/jetty-http-9.2.10.v20150310.jar build 20-Nov-2024 00:08:28 11/alt/groovy-macro-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/commons-discovery.jar build 20-Nov-2024 00:08:28 11/alt/biojava-ontology-4.1.0.jar build 20-Nov-2024 00:08:28 11/alt/jetty-io-9.2.10.v20150310.jar build 20-Nov-2024 00:08:28 11/alt/istack-commons-runtime.jar build 20-Nov-2024 00:08:28 11/alt/jersey-json-1.19.4.jar build 20-Nov-2024 00:08:28 11/alt/gmbal-api-only-MODULE.jar build 20-Nov-2024 00:08:28 11/alt/javax.xml.soap-api-1.4.0.jar build 20-Nov-2024 00:08:28 11/alt/groovy-testng-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/groovy-groovysh-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/commons-codec-1.3.jar build 20-Nov-2024 00:08:28 11/alt/jetty-server-9.2.10.v20150310.jar build 20-Nov-2024 00:08:28 11/alt/javaparser-core-3.25.5.jar build 20-Nov-2024 00:08:28 11/alt/jfreesvg-3.4.3.jar build 20-Nov-2024 00:08:28 11/alt/log4j-slf4j18-impl-2.17.1.jar build 20-Nov-2024 00:08:28 11/alt/commons-logging-1.1.1.jar build 20-Nov-2024 00:08:28 11/alt/slf4j-nop-1.7.36.jar build 20-Nov-2024 00:08:28 11/alt/groovy-sql-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/VARNAv3-93.jar build 20-Nov-2024 00:08:28 11/alt/json-simple-1.1.1.jar build 20-Nov-2024 00:08:28 11/alt/flatlaf-3.2.jar build 20-Nov-2024 00:08:28 11/alt/FastInfoset.jar build 20-Nov-2024 00:08:28 11/alt/groovy-jsr223-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/javax.annotation-api-1.3.2.jar build 20-Nov-2024 00:08:28 11/alt/javax.xml.rpc-api-1.1.2.jar build 20-Nov-2024 00:08:28 11/alt/groovy-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/jsoup-1.8.1.jar build 20-Nov-2024 00:08:28 11/alt/biojava-core-4.1.0.jar build 20-Nov-2024 00:08:28 11/alt/jaxb-api-2.3.1.jar build 20-Nov-2024 00:08:28 11/alt/groovy-cli-commons-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/jalview.jar build 20-Nov-2024 00:08:28 11/alt/jersey-client-1.19.4.jar build 20-Nov-2024 00:08:28 11/alt/javax.servlet-api-4.0.1.jar build 20-Nov-2024 00:08:28 11/alt/policy-2.7.6.jar build 20-Nov-2024 00:08:28 11/alt/xercesImpl.jar build 20-Nov-2024 00:08:28 11/alt/groovy-yaml-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/flatlaf-extras-3.2.jar build 20-Nov-2024 00:08:28 11/alt/groovy-typecheckers-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/groovy-xml-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/groovy-toml-4.0.15.jar build 20-Nov-2024 00:08:28 11/alt/jetty-util-9.2.10.v20150310.jar build 20-Nov-2024 00:08:29 11/alt/slf4j-api-1.7.36.jar build 20-Nov-2024 00:08:29 11/alt/jersey-core-1.19.4.jar build 20-Nov-2024 00:08:29 11/alt/txw2-2.3.2.jar build 20-Nov-2024 00:08:29 11/alt/jswingreader-0.3.jar build 20-Nov-2024 00:08:29 11/alt/groovy-ginq-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/groovy-templates-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/intervalstore-v1.1.jar build 20-Nov-2024 00:08:29 11/alt/groovy-jmx-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/getdown-core.jar build 20-Nov-2024 00:08:29 11/alt/jsr311-api-1.1.1.jar build 20-Nov-2024 00:08:29 11/alt/jaxws-rt-java9.jar build 20-Nov-2024 00:08:29 11/alt/groovy-swing-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/groovy-macro-library-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/vamsas-client.jar build 20-Nov-2024 00:08:29 11/alt/httpmime-4.0.3.jar build 20-Nov-2024 00:08:29 11/alt/htsjdk-2.23.0.jar build 20-Nov-2024 00:08:29 11/alt/stax-ex-1.8.1.jar build 20-Nov-2024 00:08:29 11/alt/build_properties build 20-Nov-2024 00:08:29 11/alt/groovy-docgenerator-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/groovy-cli-picocli-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/stax2-api-4.2.jar build 20-Nov-2024 00:08:29 11/alt/groovy-datetime-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/java-json.jar build 20-Nov-2024 00:08:29 11/alt/log4j-api-2.17.1.jar build 20-Nov-2024 00:08:29 11/alt/libquaqua-8.0.jnilib.jar build 20-Nov-2024 00:08:29 11/alt/mimepull-1.9.11.jar build 20-Nov-2024 00:08:29 11/alt/groovy-contracts-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/groovy-test-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/jhall.jar build 20-Nov-2024 00:08:29 11/alt/groovy-servlet-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/jabaws-min-client-NO_LOG4J-2.2.1.jar build 20-Nov-2024 00:08:29 11/alt/groovy-dateutil-4.0.15.jar build 20-Nov-2024 00:08:29 11/alt/libquaqua64-8.0.jnilib.jar build 20-Nov-2024 00:08:29 11/alt/miglayout-4.0-swing.jar build 20-Nov-2024 00:08:29 11/alt/streambuffer-1.5.7.jar build 20-Nov-2024 00:08:29 11/alt/javax.jws-api-1.1.jar build 20-Nov-2024 00:08:29 11/alt/wsdl4j-1.6.3.jar build 20-Nov-2024 00:08:29 11/resource/ build 20-Nov-2024 00:08:29 11/resource/jalview_test-release_getdown_background_error.png build 20-Nov-2024 00:08:29 11/resource/jalview_test-release_getdown_background_initialising.png build 20-Nov-2024 00:08:29 11/resource/jalview_test-release_logo.png build 20-Nov-2024 00:08:29 11/resource/jalview_test-release_logo.icns build 20-Nov-2024 00:08:29 11/resource/jalview_getdown_progress_bar.png build 20-Nov-2024 00:08:29 11/resource/jalview_test-release_getdown_background.png build 20-Nov-2024 00:08:29 11/resource/getdown-core.jar build 20-Nov-2024 00:08:29 11/getdown-launcher.jar build 20-Nov-2024 00:08:29 11/getdown.txt build 20-Nov-2024 00:08:29 11/bin/ build 20-Nov-2024 00:08:29 11/bin/update.sh build 20-Nov-2024 00:08:29 11/bin/jalview.ps1 build 20-Nov-2024 00:08:29 11/bin/update.ps1 build 20-Nov-2024 00:08:29 11/bin/jalview_test_update.ps1 build 20-Nov-2024 00:08:29 11/bin/jalview_test.ps1 build 20-Nov-2024 00:08:29 11/bin/jalview_test_update.bat build 20-Nov-2024 00:08:29 11/bin/jalview_test.bat build 20-Nov-2024 00:08:29 11/bin/jalview.sh build 20-Nov-2024 00:08:29 11/digest.txt build 20-Nov-2024 00:08:29 1.8/ build 20-Nov-2024 00:08:29 1.8/channel_launch-test-release.jvl build 20-Nov-2024 00:08:29 1.8/install/ build 20-Nov-2024 00:08:29 1.8/install/build_properties build 20-Nov-2024 00:08:29 1.8/install/getdown-launcher.jar build 20-Nov-2024 00:08:29 1.8/install/getdown.txt build 20-Nov-2024 00:08:29 1.8/digest2.txt build 20-Nov-2024 00:08:29 1.8/channel.props build 20-Nov-2024 00:08:29 1.8/getdown-launcher-new.jar build 20-Nov-2024 00:08:29 1.8/alt/ build 20-Nov-2024 00:08:29 1.8/alt/Jmol-NO_LOG4J-14.31.53.jar build 20-Nov-2024 00:08:29 1.8/alt/log4j-core-2.17.1.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-ant-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/apache-mime4j-0.6.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-console-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/axis.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-nio-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-astbuilder-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/commons-math3-3.6.1.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-json-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/httpclient-4.0.3.jar build 20-Nov-2024 00:08:29 1.8/alt/jaxrpc.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-groovydoc-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/httpcore-4.0.1.jar build 20-Nov-2024 00:08:29 1.8/alt/groovy-test-junit5-4.0.15.jar build 20-Nov-2024 00:08:29 1.8/alt/regex.jar build 20-Nov-2024 00:08:29 1.8/alt/jetty-http-9.2.10.v20150310.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-macro-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/commons-discovery.jar build 20-Nov-2024 00:08:30 1.8/alt/biojava-ontology-4.1.0.jar build 20-Nov-2024 00:08:30 1.8/alt/jetty-io-9.2.10.v20150310.jar build 20-Nov-2024 00:08:30 1.8/alt/jersey-json-1.19.4.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-testng-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-groovysh-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/commons-codec-1.3.jar build 20-Nov-2024 00:08:30 1.8/alt/jetty-server-9.2.10.v20150310.jar build 20-Nov-2024 00:08:30 1.8/alt/javaparser-core-3.25.5.jar build 20-Nov-2024 00:08:30 1.8/alt/jfreesvg-3.4.3.jar build 20-Nov-2024 00:08:30 1.8/alt/log4j-slf4j18-impl-2.17.1.jar build 20-Nov-2024 00:08:30 1.8/alt/commons-logging-1.1.1.jar build 20-Nov-2024 00:08:30 1.8/alt/slf4j-nop-1.7.36.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-sql-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/VARNAv3-93.jar build 20-Nov-2024 00:08:30 1.8/alt/json-simple-1.1.1.jar build 20-Nov-2024 00:08:30 1.8/alt/flatlaf-3.2.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-jsr223-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/jsoup-1.8.1.jar build 20-Nov-2024 00:08:30 1.8/alt/biojava-core-4.1.0.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-cli-commons-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/jalview.jar build 20-Nov-2024 00:08:30 1.8/alt/wsdl4j.jar build 20-Nov-2024 00:08:30 1.8/alt/jersey-client-1.19.4.jar build 20-Nov-2024 00:08:30 1.8/alt/xercesImpl.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-yaml-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/flatlaf-extras-3.2.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-typecheckers-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/servlet-api-3.1.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-xml-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-toml-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/jetty-util-9.2.10.v20150310.jar build 20-Nov-2024 00:08:30 1.8/alt/xml-apis.jar build 20-Nov-2024 00:08:30 1.8/alt/slf4j-api-1.7.36.jar build 20-Nov-2024 00:08:30 1.8/alt/jersey-core-1.19.4.jar build 20-Nov-2024 00:08:30 1.8/alt/jswingreader-0.3.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-ginq-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-templates-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/activation.jar build 20-Nov-2024 00:08:30 1.8/alt/intervalstore-v1.1.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-jmx-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/getdown-core.jar build 20-Nov-2024 00:08:30 1.8/alt/jsr311-api-1.1.1.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-swing-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/groovy-macro-library-4.0.15.jar build 20-Nov-2024 00:08:30 1.8/alt/vamsas-client.jar build 20-Nov-2024 00:08:30 1.8/alt/saaj.jar build 20-Nov-2024 00:08:30 1.8/alt/httpmime-4.0.3.jar build 20-Nov-2024 00:08:30 1.8/alt/htsjdk-2.23.0.jar build 20-Nov-2024 00:08:31 1.8/alt/build_properties build 20-Nov-2024 00:08:31 1.8/alt/groovy-docgenerator-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/mail.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-cli-picocli-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-datetime-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/java-json.jar build 20-Nov-2024 00:08:31 1.8/alt/log4j-api-2.17.1.jar build 20-Nov-2024 00:08:31 1.8/alt/libquaqua-8.0.jnilib.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-contracts-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-test-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/jhall.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-servlet-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/jabaws-min-client-NO_LOG4J-2.2.1.jar build 20-Nov-2024 00:08:31 1.8/alt/groovy-dateutil-4.0.15.jar build 20-Nov-2024 00:08:31 1.8/alt/libquaqua64-8.0.jnilib.jar build 20-Nov-2024 00:08:31 1.8/alt/miglayout-4.0-swing.jar build 20-Nov-2024 00:08:31 1.8/resource/ build 20-Nov-2024 00:08:31 1.8/resource/jalview_test-release_getdown_background_error.png build 20-Nov-2024 00:08:31 1.8/resource/jalview_test-release_getdown_background_initialising.png build 20-Nov-2024 00:08:31 1.8/resource/jalview_test-release_logo.png build 20-Nov-2024 00:08:31 1.8/resource/jalview_test-release_logo.icns build 20-Nov-2024 00:08:31 1.8/resource/jalview_getdown_progress_bar.png build 20-Nov-2024 00:08:31 1.8/resource/jalview_test-release_getdown_background.png build 20-Nov-2024 00:08:31 1.8/resource/getdown-core.jar build 20-Nov-2024 00:08:31 1.8/getdown-launcher.jar build 20-Nov-2024 00:08:31 1.8/getdown.txt build 20-Nov-2024 00:08:31 1.8/bin/ build 20-Nov-2024 00:08:31 1.8/bin/update.sh build 20-Nov-2024 00:08:31 1.8/bin/jalview.ps1 build 20-Nov-2024 00:08:31 1.8/bin/update.ps1 build 20-Nov-2024 00:08:31 1.8/bin/jalview_test_update.ps1 build 20-Nov-2024 00:08:31 1.8/bin/jalview_test.ps1 build 20-Nov-2024 00:08:31 1.8/bin/jalview_test_update.bat build 20-Nov-2024 00:08:31 1.8/bin/jalview_test.bat build 20-Nov-2024 00:08:31 1.8/bin/jalview.sh build 20-Nov-2024 00:08:31 1.8/digest.txt simple 20-Nov-2024 00:08:31 Finished task 'Create tar of getdown ${bamboo.CHANNEL} channel website' with result: Success command 20-Nov-2024 00:08:31 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE simple 20-Nov-2024 00:08:31 Starting task 'Create tar of DEVELOP channel executable jar' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 20-Nov-2024 00:08:31 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-6911965257015950126.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_repository_46497969_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GTC0-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=29\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_4=/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-4202243983555396046.sh\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_7=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 --info eclipse jalviewjsCreateJ2sSettings jalviewjs\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GTC0 clean getdown shadowJar\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_8=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=1.8 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 getdown shadowJar\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\n build 20-Nov-2024 00:08:31 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1/build build 20-Nov-2024 00:08:31 executable_jar/ build 20-Nov-2024 00:08:31 executable_jar/jalview-all-2.11.4.1-test-j1.8.jar.sha256 build 20-Nov-2024 00:08:31 executable_jar/jalview-all-2.11.4.1-test-j11.jar.sha256 build 20-Nov-2024 00:08:31 executable_jar/jalview-all-2.11.4.1-test-j11.jar build 20-Nov-2024 00:08:33 executable_jar/jalview-all-2.11.4.1-test-j1.8.jar simple 20-Nov-2024 00:08:34 Finished task 'Create tar of DEVELOP channel executable jar' with result: Success command 20-Nov-2024 00:08:34 Substituting variable: ${bamboo.CHANNEL} with TEST-RELEASE simple 20-Nov-2024 00:08:34 Starting task 'create tar of JalviewJS site' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 20-Nov-2024 00:08:34 Beginning to execute external process for build 'Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job #29 (JB-GTC0-JOB1-29)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-7835243912566932676.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_repository_46497969_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GTC0-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=29\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_repository_46497969_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GTC0-JOB1-29\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GTC0\nbamboo_repository_46497969_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_repository_46497969_name=Jalview Git\nbamboo_buildTimeStamp=2024-11-20T00:00:00.126Z\nbamboo_repository_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_5=/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-6911965257015950126.sh\nbamboo_build_commandline_com_atlassian_bamboo_plugins_scripttask_task_builder_script_4=/srv/bamboo/bamboo-home/temp/JB-GTC0-JOB1-29-ScriptBuildTask-4202243983555396046.sh\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GTC0-JOB1-29\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown TEST_RELEASE Channel - releases-Release_2_11_4_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_CHANNEL=TEST-RELEASE\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46497969_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_7=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 --info eclipse jalviewjsCreateJ2sSettings jalviewjs\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GTC0 clean getdown shadowJar\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301537\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46497969_branch_name=releases/Release_2_11_4_Branch\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GTC0-JOB1\nbamboo_planKey=JB-GTC0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_8=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=TEST-RELEASE -PJAVA_VERSION=1.8 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GTC0 getdown shadowJar\nbamboo_repository_46497969_previous_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\n build 20-Nov-2024 00:08:34 total 288 build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:07 _ build 20-Nov-2024 00:08:34 -rw-r--r-- 1 bamboo bamboo 150 Nov 20 00:08 AmbiguityCodes.dat build 20-Nov-2024 00:08:34 -rw-r--r-- 1 bamboo bamboo 474 Nov 20 00:08 authors.props build 20-Nov-2024 00:08:34 -rw-r--r-- 1 bamboo bamboo 905 Nov 20 00:08 channel.props build 20-Nov-2024 00:08:34 drwxr-xr-x 5 bamboo bamboo 4096 Nov 20 00:07 com build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 core build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 darrylbu build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 default_images build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:07 _ES6 build 20-Nov-2024 00:08:34 drwxr-xr-x 4 bamboo bamboo 4096 Nov 20 00:07 ext build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 fr build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 fts build 20-Nov-2024 00:08:34 -rw-r--r-- 1 bamboo bamboo 15295 Nov 20 00:08 GeneticCodes.dat build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 gnu build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 gov build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 images build 20-Nov-2024 00:08:34 drwxr-xr-x 5 bamboo bamboo 4096 Nov 20 00:07 intervalstore build 20-Nov-2024 00:08:34 drwxr-xr-x 33 bamboo bamboo 4096 Nov 20 00:07 jalview build 20-Nov-2024 00:08:34 drwxr-xr-x 15 bamboo bamboo 4096 Nov 20 00:07 java build 20-Nov-2024 00:08:34 drwxr-xr-x 8 bamboo bamboo 4096 Nov 20 00:07 javajs build 20-Nov-2024 00:08:34 drwxr-xr-x 11 bamboo bamboo 4096 Nov 20 00:07 javax build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 lang build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:07 mc_view build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 net build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 netscape build 20-Nov-2024 00:08:34 drwxr-xr-x 12 bamboo bamboo 4096 Nov 20 00:07 org build 20-Nov-2024 00:08:34 drwxr-xr-x 4 bamboo bamboo 4096 Nov 20 00:07 resources build 20-Nov-2024 00:08:34 drwxr-xr-x 2 bamboo bamboo 4096 Nov 20 00:08 scoreModel build 20-Nov-2024 00:08:34 -rw-r--r-- 1 bamboo bamboo 144326 Nov 20 00:08 so-xp-simple.obo.zip build 20-Nov-2024 00:08:34 drwxr-xr-x 15 bamboo bamboo 4096 Nov 20 00:07 sun build 20-Nov-2024 00:08:34 drwxr-xr-x 10 bamboo bamboo 4096 Nov 20 00:07 swingjs build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 uk build 20-Nov-2024 00:08:34 drwxr-xr-x 3 bamboo bamboo 4096 Nov 20 00:07 vamsas build 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jalview-js/swingjs/j2s/sun/util/resources/sk/CurrencyNames_sk_SK.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/sk/CalendarData_sk.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/sq/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/sq/CurrencyNames_sq_AL.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/sq/CalendarData_sq.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/sq/LocaleNames_sq.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/TimeZoneNames_ja.js build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/CurrencyNames_ja.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/LocaleNames_ja.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/CurrencyNames_ja_JP.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ja/CalendarData_ja.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_US.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_EC.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CalendarData_es.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_CU.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_GT.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_CR.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/TimeZoneNames_es.js build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_NI.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_HN.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_VE.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_PA.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_MX.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_PY.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_UY.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_AR.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_SV.properties 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jalview-js/swingjs/j2s/sun/util/resources/es/CurrencyNames_es_BO.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/es/CalendarData_es_ES.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ms/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ms/LocaleNames_ms.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ms/CalendarData_ms_MY.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ms/CurrencyNames_ms_MY.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/in/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/in/LocaleNames_in.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/in/CurrencyNames_in_ID.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/in/CalendarData_in_ID.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ga/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ga/CurrencyNames_ga_IE.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/ga/LocaleNames_ga.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/TimeZoneNames.js build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/LocaleNames.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/CurrencyNames_fr_CA.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/TimeZoneNames_fr.js build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/CurrencyNames_fr.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/CalendarData_fr.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/fr/CurrencyNames_fr_FR.properties build 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jalview-js/swingjs/j2s/sun/util/resources/lv/CalendarData_lv.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/lv/LocaleNames_lv.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/lv/CurrencyNames_lv_LV.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/th/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/th/CalendarData_th.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/th/CurrencyNames_th_TH.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/th/LocaleNames_th.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/tr/ build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/tr/CalendarData_tr.properties build 20-Nov-2024 00:08:40 jalview-js/swingjs/j2s/sun/util/resources/tr/CurrencyNames_tr_TR.properties build 20-Nov-2024 00:08:40 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build results summary... simple 20-Nov-2024 00:08:43 Saving build results to disk... simple 20-Nov-2024 00:08:43 Logging substituted variables... simple 20-Nov-2024 00:08:43 Indexing build results... simple 20-Nov-2024 00:08:43 Finished building JB-GTC0-JOB1-29.