Build: #3 was successful
Job: Clover and Tests was successful
Build log
The build generated 2,189 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3576intervalStore_1_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-34_comparing_msas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4366_foldseek_3di_viewing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/hmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/mchmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4381_dynamic_value_colouring_of_annotations does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/JAL-4366_3di_msa_forfoldseeks does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 |
| 30-Aug-2024 09:53:01 | + e340907...32915e0 spike/JAL-4386_merge_multiple_leaves -> origin/spike/JAL-4386_merge_multiple_leaves (forced update) |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3576intervalStore_1_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-34_comparing_msas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-4366_foldseek_3di_viewing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/hmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/mchmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/improvement/JAL-4381_dynamic_value_colouring_of_annotations does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 30-Aug-2024 09:53:01 | 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! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/JAL-4366_3di_msa_forfoldseeks does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 30-Aug-2024 09:53:01 | Already on 'spike/JAL-4386_merge_multiple_leaves' |
| 30-Aug-2024 09:53:01 | Your branch is ahead of 'origin/spike/JAL-4386_merge_multiple_leaves' by 1 commit. |
| 30-Aug-2024 09:53:01 | (use "git push" to publish your local commits) |
| 30-Aug-2024 09:53:01 | HEAD is now at 32915e0 JAL-4386 Merge multiple leaves for ss source |
| 30-Aug-2024 09:53:01 | Updated source code to revision: 32915e0cc33a6386b148db7e1f78ee4c1369fd7b |
| 30-Aug-2024 09:53:01 | Finished task 'Checkout Default Repository' with result: Success |
| 30-Aug-2024 09:53:01 | Running pre-build action: VCS Version Collector |
| 30-Aug-2024 09:53:01 | Running pre-build action: Artifactory Release Staging |
| 30-Aug-2024 09:53:01 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 30-Aug-2024 09:53:01 | Bamboo Artifactory Plugin version: 2.6.2 |
| 30-Aug-2024 09:53:01 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves - Clover and Tests #3 (JB-GDB607-JOB1-3)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/JAL-4386_merge_multiple_leaves bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/JAL-4386_merge_multiple_leaves bamboo_repository_revision_number=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB607-JOB1-3 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB607-JOB1 bamboo_shortPlanName=spike-JAL-4386_merge_multiple_leaves bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=3 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB607-JOB1-3 bamboo_repository_46498004_git_username= bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves bamboo_shortPlanKey=GDB607 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_buildTimeStamp=2024-08-30T09:53:01.650+01:00 bamboo_repository_previous_revision_number=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_planRepository_previousRevision=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_repository_46498004_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_46498004_revision_number=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_repository_git_branch=spike/JAL-4386_merge_multiple_leaves bamboo_buildResultKey=JB-GDB607-JOB1-3 bamboo_repository_branch_name=spike/JAL-4386_merge_multiple_leaves bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=32915e0cc33a6386b148db7e1f78ee4c1369fd7b SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_46498004_name=Jalview Git LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=spike/JAL-4386_merge_multiple_leaves bamboo_repository_46498004_previous_revision_number=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_planRepository_branchDisplayName=spike/JAL-4386_merge_multiple_leaves bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/JAL-4386_merge_multiple_leaves _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301607 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_repository_46498004_git_branch=spike/JAL-4386_merge_multiple_leaves bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 bamboo_planKey=JB-GDB607 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498004_branch_name=spike/JAL-4386_merge_multiple_leaves HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/JAL-4386_merge_multiple_leaves PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 30-Aug-2024 09:53:01 | 444 |
| 30-Aug-2024 09:53:03 | |
| 30-Aug-2024 09:53:03 | > Configure project : |
| 30-Aug-2024 09:53:03 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 30-Aug-2024 09:53:03 | JALVIEW_VERSION is set to '2.11.4.0' |
| 30-Aug-2024 09:53:03 | HEADLESS BUILD |
| 30-Aug-2024 09:53:03 | J2S ENABLED |
| 30-Aug-2024 09:53:03 | Using a LOCAL profile. |
| 30-Aug-2024 09:53:03 | eclipseDir exists |
| 30-Aug-2024 09:53:03 | |
| 30-Aug-2024 09:53:03 | > Task :clean |
| 30-Aug-2024 09:53:03 | > Task :cleanClover |
| 30-Aug-2024 09:53:03 | > Task :cleanTest UP-TO-DATE |
| 30-Aug-2024 09:53:05 | |
| 30-Aug-2024 09:53:05 | > Task :cloverInstrJava |
| 30-Aug-2024 09:53:05 | Clover: About to instrument 1101 files |
| 30-Aug-2024 09:53:05 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 30-Aug-2024 09:53:05 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover.db'. |
| 30-Aug-2024 09:53:05 | Processing files at 1.9 source level. |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:08 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 30-Aug-2024 09:53:15 | Clover all over. Instrumented 1101 files (111 packages). |
| 30-Aug-2024 09:53:17 | |
| 30-Aug-2024 09:53:17 | > Task :cloverInstrTests |
| 30-Aug-2024 09:53:17 | Clover: About to instrument test files |
| 30-Aug-2024 09:53:17 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 30-Aug-2024 09:53:17 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover.db'. |
| 30-Aug-2024 09:53:17 | Processing files at 1.9 source level. |
| 30-Aug-2024 09:53:20 | Clover all over. Instrumented 290 files (52 packages). |
| 30-Aug-2024 09:53:20 | 1592 test methods detected. |
| 30-Aug-2024 09:53:20 | |
| 30-Aug-2024 09:53:20 | > Task :cloverInstr |
| 30-Aug-2024 09:53:22 | |
| 30-Aug-2024 09:53:22 | > Task :compileCloverJava |
| 30-Aug-2024 09:53:22 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 30-Aug-2024 09:53:22 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' 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. |
| 30-Aug-2024 09:53:22 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' 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. |
| 30-Aug-2024 09:53:22 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' 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. |
| 30-Aug-2024 09:53:22 | Setting target compatibility to 11 |
| 30-Aug-2024 09:53:36 | Note: Some input files use or override a deprecated API. |
| 30-Aug-2024 09:53:36 | Note: Recompile with -Xlint:deprecation for details. |
| 30-Aug-2024 09:53:36 | Note: Some input files use unchecked or unsafe operations. |
| 30-Aug-2024 09:53:36 | Note: Recompile with -Xlint:unchecked for details. |
| 30-Aug-2024 09:53:39 | |
| 30-Aug-2024 09:53:39 | > Task :processCloverResources NO-SOURCE |
| 30-Aug-2024 09:53:39 | > Task :cloverClasses |
| 30-Aug-2024 09:53:40 | > Task :copyHelp |
| 30-Aug-2024 09:53:41 | > Task :buildIndices |
| 30-Aug-2024 09:53:41 | > Task :copyResources |
| 30-Aug-2024 09:53:41 | > Task :copyChannelResources |
| 30-Aug-2024 09:53:41 | |
| 30-Aug-2024 09:53:41 | > Task :createBuildProperties |
| 30-Aug-2024 09:53:41 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 30-Aug-2024 09:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-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. |
| 30-Aug-2024 09:53:41 | |
| 30-Aug-2024 09:53:41 | > Task :buildResources |
| 30-Aug-2024 09:53:41 | > Task :copyDocs |
| 30-Aug-2024 09:53:41 | |
| 30-Aug-2024 09:53:41 | > Task :convertMdFiles |
| 30-Aug-2024 09:53:41 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 30-Aug-2024 09:53:41 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 30-Aug-2024 09:53:41 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 30-Aug-2024 09:53:41 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build/doc/building.html |
| 30-Aug-2024 09:53:41 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 30-Aug-2024 09:53:41 | |
| 30-Aug-2024 09:53:41 | > Task :releasesTemplates |
| 30-Aug-2024 09:53:41 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 30-Aug-2024 09:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-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. |
| 30-Aug-2024 09:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-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. |
| 30-Aug-2024 09:53:41 | |
| 30-Aug-2024 09:53:41 | > Task :prepare |
| 30-Aug-2024 09:53:43 | |
| 30-Aug-2024 09:53:43 | > Task :compileJava |
| 30-Aug-2024 09:53:43 | Setting target compatibility to 11 |
| 30-Aug-2024 09:53:48 | Note: Some input files use or override a deprecated API. |
| 30-Aug-2024 09:53:48 | Note: Recompile with -Xlint:deprecation for details. |
| 30-Aug-2024 09:53:48 | Note: Some input files use unchecked or unsafe operations. |
| 30-Aug-2024 09:53:48 | Note: Recompile with -Xlint:unchecked for details. |
| 30-Aug-2024 09:53:50 | |
| 30-Aug-2024 09:53:50 | > Task :compileTestJava |
| 30-Aug-2024 09:53:50 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 30-Aug-2024 09:53:50 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' 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. |
| 30-Aug-2024 09:53:50 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' 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. |
| 30-Aug-2024 09:53:50 | Setting target compatibility to 11 |
| 30-Aug-2024 09:53:55 | Note: Some input files use or override a deprecated API. |
| 30-Aug-2024 09:53:55 | Note: Recompile with -Xlint:deprecation for details. |
| 30-Aug-2024 09:53:55 | Note: Some input files use unchecked or unsafe operations. |
| 30-Aug-2024 09:53:55 | Note: Recompile with -Xlint:unchecked for details. |
| 30-Aug-2024 09:53:56 | |
| 30-Aug-2024 09:53:56 | > Task :processTestResources |
| 30-Aug-2024 09:53:56 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 30-Aug-2024 09:53:56 | |
| 30-Aug-2024 09:53:56 | > Task :testClasses |
| 30-Aug-2024 09:53:58 | |
| 30-Aug-2024 09:53:58 | > Task :testTask0 |
| 30-Aug-2024 09:53:58 | Running tests WITH clover |
| 30-Aug-2024 09:54:00 | WARNING: An illegal reflective access operation has occurred |
| 30-Aug-2024 09:54:00 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 30-Aug-2024 09:54:00 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 30-Aug-2024 09:54:00 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 30-Aug-2024 09:54:00 | WARNING: All illegal access operations will be denied in a future release |
| 30-Aug-2024 09:57:52 | |
| 30-Aug-2024 09:57:52 | > Task :testTask1 |
| 30-Aug-2024 09:57:52 | Running tests WITH clover |
| 30-Aug-2024 09:57:53 | WARNING: An illegal reflective access operation has occurred |
| 30-Aug-2024 09:57:53 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 30-Aug-2024 09:57:53 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 30-Aug-2024 09:57:53 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 30-Aug-2024 09:57:53 | WARNING: All illegal access operations will be denied in a future release |
| 30-Aug-2024 09:59:28 | |
| 30-Aug-2024 09:59:28 | > Task :testTask2 |
| 30-Aug-2024 09:59:28 | Running tests WITH clover |
| 30-Aug-2024 09:59:31 | |
| 30-Aug-2024 09:59:31 | > Task :testTask3 |
| 30-Aug-2024 09:59:31 | Running tests WITH clover |
| 30-Aug-2024 09:59:33 | WARNING: An illegal reflective access operation has occurred |
| 30-Aug-2024 09:59:33 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 30-Aug-2024 09:59:33 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 30-Aug-2024 09:59:33 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 30-Aug-2024 09:59:33 | WARNING: All illegal access operations will be denied in a future release |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | > Task :test NO-SOURCE |
| 30-Aug-2024 10:00:18 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 30-Aug-2024 10:00:18 | │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 54.051 seconds │ |
| 30-Aug-2024 10:00:18 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/tests/testTask0/index.html│ |
| 30-Aug-2024 10:00:18 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 30-Aug-2024 10:00:18 | │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.575 seconds │ |
| 30-Aug-2024 10:00:18 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/tests/testTask1/index.html│ |
| 30-Aug-2024 10:00:18 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 30-Aug-2024 10:00:18 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.638 seconds │ |
| 30-Aug-2024 10:00:18 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/tests/testTask2/index.html│ |
| 30-Aug-2024 10:00:18 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 30-Aug-2024 10:00:18 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.385 seconds │ |
| 30-Aug-2024 10:00:18 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/tests/testTask3/index.html│ |
| 30-Aug-2024 10:00:18 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 30-Aug-2024 10:00:18 | │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 141.649 seconds │ |
| 30-Aug-2024 10:00:18 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 30-Aug-2024 10:00:18 | Please consult deprecation warnings for more details. |
| 30-Aug-2024 10:00:18 | |
| 30-Aug-2024 10:00:18 | BUILD SUCCESSFUL in 7m 16s |
| 30-Aug-2024 10:00:18 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 30-Aug-2024 10:00:18 | Finished task 'Run tests with openclover under gradle' with result: Success |
| 30-Aug-2024 10:00:18 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 30-Aug-2024 10:00:18 | Bamboo Artifactory Plugin version: 2.6.2 |
| 30-Aug-2024 10:00:18 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves - Clover and Tests #3 (JB-GDB607-JOB1-3)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/JAL-4386_merge_multiple_leaves bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/JAL-4386_merge_multiple_leaves bamboo_repository_revision_number=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB607-JOB1-3 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB607-JOB1 bamboo_shortPlanName=spike-JAL-4386_merge_multiple_leaves bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=3 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB607-JOB1-3 bamboo_repository_46498004_git_username= bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves bamboo_shortPlanKey=GDB607 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_buildTimeStamp=2024-08-30T09:53:01.650+01:00 bamboo_repository_previous_revision_number=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_planRepository_previousRevision=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_repository_46498004_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_46498004_revision_number=32915e0cc33a6386b148db7e1f78ee4c1369fd7b bamboo_repository_git_branch=spike/JAL-4386_merge_multiple_leaves bamboo_buildResultKey=JB-GDB607-JOB1-3 bamboo_repository_branch_name=spike/JAL-4386_merge_multiple_leaves bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_multiple_leaves - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=32915e0cc33a6386b148db7e1f78ee4c1369fd7b SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_46498004_name=Jalview Git LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=spike/JAL-4386_merge_multiple_leaves bamboo_repository_46498004_previous_revision_number=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=false bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=e340907f86006b014c2f28b8b2054fa908b594ad bamboo_planRepository_branchDisplayName=spike/JAL-4386_merge_multiple_leaves bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/JAL-4386_merge_multiple_leaves _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301607 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_repository_46498004_git_branch=spike/JAL-4386_merge_multiple_leaves bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1 bamboo_planKey=JB-GDB607 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498004_branch_name=spike/JAL-4386_merge_multiple_leaves HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/JAL-4386_merge_multiple_leaves PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 30-Aug-2024 10:00:18 | 444 |
| 30-Aug-2024 10:00:25 | |
| 30-Aug-2024 10:00:25 | > Configure project : |
| 30-Aug-2024 10:00:25 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 30-Aug-2024 10:00:25 | JALVIEW_VERSION is set to '2.11.4.0' |
| 30-Aug-2024 10:00:25 | HEADLESS BUILD |
| 30-Aug-2024 10:00:25 | J2S ENABLED |
| 30-Aug-2024 10:00:25 | Using a LOCAL profile. |
| 30-Aug-2024 10:00:26 | eclipseDir exists |
| 30-Aug-2024 10:00:28 | |
| 30-Aug-2024 10:00:28 | > Task :cloverHtmlReport |
| 30-Aug-2024 10:00:28 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 30-Aug-2024 10:00:29 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/clover' |
| 30-Aug-2024 10:01:09 | Done. Processed 115 packages in 39517ms (343ms per package). |
| 30-Aug-2024 10:01:14 | |
| 30-Aug-2024 10:01:14 | > Task :cloverXmlReport |
| 30-Aug-2024 10:01:14 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 30-Aug-2024 10:01:14 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/clover/clover.xml' |
| 30-Aug-2024 10:01:15 | |
| 30-Aug-2024 10:01:15 | > Task :cloverReport |
| 30-Aug-2024 10:01:15 | |
| 30-Aug-2024 10:01:15 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 30-Aug-2024 10:01:15 | |
| 30-Aug-2024 10:01:15 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 30-Aug-2024 10:01:15 | |
| 30-Aug-2024 10:01:15 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 30-Aug-2024 10:01:15 | |
| 30-Aug-2024 10:01:15 | BUILD SUCCESSFUL in 56s |
| 30-Aug-2024 10:01:15 | 2 actionable tasks: 2 executed |
| 30-Aug-2024 10:01:15 | Finished task 'Clover Report' with result: Success |
| 30-Aug-2024 10:01:15 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 30-Aug-2024 10:01:15 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1... |
| 30-Aug-2024 10:01:15 | Finished task 'TestNG Parser' with result: Success |
| 30-Aug-2024 10:01:15 | Running post build plugin 'NCover Results Collector' |
| 30-Aug-2024 10:01:15 | Running post build plugin 'Artifact Copier' |
| 30-Aug-2024 10:01:15 | Publishing an artifact: Clover Report (System) |
| 30-Aug-2024 10:01:16 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.478 s |
| 30-Aug-2024 10:01:16 | Publishing an artifact: TestNG report |
| 30-Aug-2024 10:01:16 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB607-JOB1/build/reports/tests/test does not exist. |
| 30-Aug-2024 10:01:16 | The artifact hasn't been successfully published after 1.367 ms |
| 30-Aug-2024 10:01:16 | Running post build plugin 'Artifactory Release Management Staging' |
| 30-Aug-2024 10:01:16 | Running post build plugin 'Artifactory Build Info Copier' |
| 30-Aug-2024 10:01:16 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 30-Aug-2024 10:01:16 | Running post build plugin 'npm Cache Cleanup' |
| 30-Aug-2024 10:01:16 | Running post build plugin 'Clover Results Collector' |
| 30-Aug-2024 10:01:16 | Running post build plugin 'Docker Container Cleanup' |
| 30-Aug-2024 10:01:16 | Finalising the build... |
| 30-Aug-2024 10:01:16 | Stopping timer. |
| 30-Aug-2024 10:01:16 | Build JB-GDB607-JOB1-3 completed. |
| 30-Aug-2024 10:01:16 | Running on server: post build plugin 'NCover Results Collector' |
| 30-Aug-2024 10:01:16 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 30-Aug-2024 10:01:16 | Running on server: post build plugin 'Clover Delta Calculator' |
| 30-Aug-2024 10:01:16 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 30-Aug-2024 10:01:16 | All post build plugins have finished |
| 30-Aug-2024 10:01:16 | Generating build results summary... |
| 30-Aug-2024 10:01:17 | Saving build results to disk... |
| 30-Aug-2024 10:01:17 | Logging substituted variables... |
| 30-Aug-2024 10:01:17 | Indexing build results... |
| 30-Aug-2024 10:01:17 | Finished building JB-GDB607-JOB1-3. |