Build: #2 was successful
Job: Default Job was successful
Build log
The build generated 2,157 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3576intervalStore_1_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4159_pasimap_JAL-4423_alt_msa_source does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4446_cancellable_pasimap_etal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-34_comparing_msas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4366_foldseek_3di_viewing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/hmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/mchmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4381_dynamic_value_colouring_of_annotations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jims/review_JAL-4409_implement_extra_schemes_in_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4386_merge_multiple_leaves does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/JAL-4366_3di_msa_forfoldseeks does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 |
| 26-Aug-2024 18:42:04 | 86c07a2..0a00266 features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 -> origin/features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 |
| 26-Aug-2024 18:42:04 | f599ef3..88ec5ec JAL-4442_cant_quit_jalview_on_windows_11 -> origin/JAL-4442_cant_quit_jalview_on_windows_11 |
| 26-Aug-2024 18:42:04 | 894e28b..88be276 develop -> origin/develop |
| 26-Aug-2024 18:42:04 | b3aa009..87ab843 feature/JAL-3631_allow_jalview_to_work_from_user-space_directory -> origin/feature/JAL-3631_allow_jalview_to_work_from_user-space_directory |
| 26-Aug-2024 18:42:04 | * [new branch] jims/JAL-4420_review_redo -> origin/jims/JAL-4420_review_redo |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-1601-direct-jpred4-rest-service does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3866_RNAalifold-slivka-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3927_ws_preferences_dialog_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-4152-typed-singleton-provider does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3445-BSML-reader does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/develop_j2s_v3_2_9_j11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3066_Jalview_212_slivka-integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3362_Jalview_212_alpha does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/JAL-3899_deuniquify_refactor does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/alpha/merge_212_JalviewJS_2112 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3807_jpred-with-slivka does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3809_ws_params_dialog_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3810_annotation_ws_stopping_abruptly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3849_aacon-parameters does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4313-make-visible-annot-fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/cherrypicks/JAL-3660_JAL-3561_JAL-3662_cli_outputformat does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/Release_2_12_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/development/Release_2_12_Branch_JAL-4102_21126_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3515-slivka-preferences does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3576intervalStore_1_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3686_slivka_client_js_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3954-ebi-phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4159_pasimap_JAL-4423_alt_msa_source does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-4446_cancellable_pasimap_etal does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-34_comparing_msas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-4366_foldseek_3di_viewing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/hmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/hmmer_statistics does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/mchmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/mchmmer_merge_JAL-1950 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4245-return-null-from-getRootDataset does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/improvement/JAL-4381_dynamic_value_colouring_of_annotations does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jims/review_JAL-4409_implement_extra_schemes_in_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-3285_mchmmer_with_211_develop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmm/JAL-4199-web-services-testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3878_ws-overhaul-3 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3954-ebi-phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4199-task-execution-update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/JAL-4199-web-services-testing does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/Release_2_12_ws_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix-slivka does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4232-disable-unavailable-services does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 26-Aug-2024 18:42:04 | 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! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-1950_hmmer3client does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/JAL-4386_merge_multiple_leaves does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/jims_dec_2022_212_merge does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/JAL-4366_3di_msa_forfoldseeks does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/tasks/JAL-3070_wsinterfaces does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/testpaches/JAL-2719_JAL-1264_testfails does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/update/JAL-4108_212_testng_jar_update does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 26-Aug-2024 18:42:04 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 26-Aug-2024 18:42:06 | Already on 'features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4' |
| 26-Aug-2024 18:42:06 | Your branch is behind 'origin/features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4' by 13 commits, and can be fast-forwarded. |
| 26-Aug-2024 18:42:06 | (use "git pull" to update your local branch) |
| 26-Aug-2024 18:42:06 | HEAD is now at 0a00266 Merge branch 'develop' into features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 |
| 26-Aug-2024 18:42:06 | Updated source code to revision: 0a00266f602cde16fddd1b297279cf9b2c13a708 |
| 26-Aug-2024 18:42:06 | Finished task 'Checkout Default Repository' with result: Success |
| 26-Aug-2024 18:42:06 | Running pre-build action: VCS Version Collector |
| 26-Aug-2024 18:42:06 | Running pre-build action: Artifactory Release Staging |
| 26-Aug-2024 18:42:06 | Substituting variable: ${bamboo.planKey} with JB-GDL13 |
| 26-Aug-2024 18:42:06 | Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 26-Aug-2024 18:42:06 | Bamboo Artifactory Plugin version: 2.6.2 |
| 26-Aug-2024 18:42:06 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 - Default Job #2 (JB-GDL13-JOB1-2)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL13 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_dependency_parent_0=JB-GDB609-2 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_dependency_parent_total=1 bamboo_planRepository_1_branchDisplayName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_repository_revision_number=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL13-JOB1-2 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-GDL13-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDL13-JOB1 bamboo_shortPlanName=features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=2 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46498017_git_username= bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL13-JOB1-2 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_shortPlanKey=GDL13 bamboo_repository_46498017_previous_revision_number=86c07a2d67f86f9b66f0c1029e3fbe3004b37d89 bamboo_shortJobKey=JOB1 bamboo_repository_46498017_name=Jalview Git bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_buildTimeStamp=2024-08-26T18:41:14.940+01:00 bamboo_repository_previous_revision_number=86c07a2d67f86f9b66f0c1029e3fbe3004b37d89 bamboo_repository_git_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_buildResultKey=JB-GDL13-JOB1-2 bamboo_repository_branch_name=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=0a00266f602cde16fddd1b297279cf9b2c13a708 SHLVL=1 bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_46498017_revision_number=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_repository_name=Jalview Git JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ 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=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_repository_46498017_git_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_branchDisplayName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 _=/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-46301633 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_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_46498017_branch_name=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 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-GDL13-JOB1 bamboo_planKey=JB-GDL13 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498017_git_repositoryUrl=http://source.jalview.org/git/jalview.git HOME=/home/bamboo bamboo_planRepository_1_branchName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 26-Aug-2024 18:42:07 | |
| 26-Aug-2024 18:42:07 | > Configure project : |
| 26-Aug-2024 18:42:07 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 26-Aug-2024 18:42:07 | JALVIEW_VERSION is set to '2.11.4.0' |
| 26-Aug-2024 18:42:07 | HEADLESS BUILD |
| 26-Aug-2024 18:42:07 | J2S ENABLED |
| 26-Aug-2024 18:42:07 | Using a BUILD profile. |
| 26-Aug-2024 18:42:07 | eclipseDir exists |
| 26-Aug-2024 18:42:07 | |
| 26-Aug-2024 18:42:07 | > Task :clean |
| 26-Aug-2024 18:42:07 | > Task :cleanPackageDir |
| 26-Aug-2024 18:42:07 | > Task :getdownImagesCopy |
| 26-Aug-2024 18:42:07 | > Task :getdownImagesProcess |
| 26-Aug-2024 18:42:07 | > Task :getdownImages |
| 26-Aug-2024 18:42:08 | > Task :copyHelp |
| 26-Aug-2024 18:42:09 | > Task :buildIndices |
| 26-Aug-2024 18:42:09 | > Task :copyResources |
| 26-Aug-2024 18:42:09 | > Task :copyChannelResources |
| 26-Aug-2024 18:42:09 | |
| 26-Aug-2024 18:42:09 | > Task :createBuildProperties |
| 26-Aug-2024 18:42:09 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 26-Aug-2024 18:42:09 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-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. |
| 26-Aug-2024 18:42:09 | |
| 26-Aug-2024 18:42:09 | > Task :buildResources |
| 26-Aug-2024 18:42:09 | > Task :copyDocs |
| 26-Aug-2024 18:42:09 | |
| 26-Aug-2024 18:42:09 | > Task :convertMdFiles |
| 26-Aug-2024 18:42:09 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 26-Aug-2024 18:42:09 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 26-Aug-2024 18:42:09 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 26-Aug-2024 18:42:09 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build/doc/building.html |
| 26-Aug-2024 18:42:09 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 26-Aug-2024 18:42:09 | |
| 26-Aug-2024 18:42:09 | > Task :releasesTemplates |
| 26-Aug-2024 18:42:09 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 26-Aug-2024 18:42:09 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-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. |
| 26-Aug-2024 18:42:09 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-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. |
| 26-Aug-2024 18:42:09 | |
| 26-Aug-2024 18:42:09 | > Task :prepare |
| 26-Aug-2024 18:42:11 | |
| 26-Aug-2024 18:42:11 | > Task :compileJava |
| 26-Aug-2024 18:42:11 | Setting target compatibility to 11 |
| 26-Aug-2024 18:42:17 | Note: Some input files use or override a deprecated API. |
| 26-Aug-2024 18:42:17 | Note: Recompile with -Xlint:deprecation for details. |
| 26-Aug-2024 18:42:17 | Note: Some input files use unchecked or unsafe operations. |
| 26-Aug-2024 18:42:17 | Note: Recompile with -Xlint:unchecked for details. |
| 26-Aug-2024 18:42:17 | |
| 26-Aug-2024 18:42:17 | > Task :processResources |
| 26-Aug-2024 18:42:17 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:17 | |
| 26-Aug-2024 18:42:17 | > Task :classes |
| 26-Aug-2024 18:42:19 | |
| 26-Aug-2024 18:42:19 | > Task :compileLinkCheck |
| 26-Aug-2024 18:42:19 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 26-Aug-2024 18:42:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 26-Aug-2024 18:42:19 | |
| 26-Aug-2024 18:42:19 | > Task :linkCheck |
| 26-Aug-2024 18:42:19 | Checking help file links |
| 26-Aug-2024 18:42:19 | |
| 26-Aug-2024 18:42:19 | Results: |
| 26-Aug-2024 18:42:19 | 156 distinct help targets |
| 26-Aug-2024 18:42:19 | 156 help mappings |
| 26-Aug-2024 18:42:19 | 0 invalid targets |
| 26-Aug-2024 18:42:19 | 31 unused targets |
| 26-Aug-2024 18:42:19 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 26-Aug-2024 18:42:19 | overviewprefs: html/features/preferences.html#overview |
| 26-Aug-2024 18:42:19 | cdnafeatures: html/features/codingfeatures.html |
| 26-Aug-2024 18:42:19 | startupprefs: html/features/preferences.html#startup |
| 26-Aug-2024 18:42:19 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 26-Aug-2024 18:42:19 | io.modellerpir: html/io/modellerpir.html |
| 26-Aug-2024 18:42:19 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 26-Aug-2024 18:42:19 | pdbmcviewer: html/features/pdbviewer.html |
| 26-Aug-2024 18:42:19 | groovy.colours: html/features/groovy.html#groovyColours |
| 26-Aug-2024 18:42:19 | seqmappings: html/features/seqmappings.html |
| 26-Aug-2024 18:42:19 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 26-Aug-2024 18:42:19 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 26-Aug-2024 18:42:19 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 26-Aug-2024 18:42:19 | search: html/features/search.html |
| 26-Aug-2024 18:42:19 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 26-Aug-2024 18:42:19 | alformats: html/io/fileformats.html |
| 26-Aug-2024 18:42:19 | strucprefs: html/features/preferences.html#structure |
| 26-Aug-2024 18:42:19 | siftsmapping: html/features/siftsmapping.html |
| 26-Aug-2024 18:42:19 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 26-Aug-2024 18:42:19 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 26-Aug-2024 18:42:19 | newkeys: html/features/newkeystrokes.html |
| 26-Aug-2024 18:42:19 | importvcf.attribs: html/features/importvcf.html#attribs |
| 26-Aug-2024 18:42:19 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 26-Aug-2024 18:42:19 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 26-Aug-2024 18:42:19 | jalarchive: html/features/jalarchive.html |
| 26-Aug-2024 18:42:19 | newsreader: html/webServices/newsreader.html |
| 26-Aug-2024 18:42:19 | jalviewcltool: html/features/commandline.html#script |
| 26-Aug-2024 18:42:19 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 26-Aug-2024 18:42:19 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 26-Aug-2024 18:42:19 | paematrixformat: html/io/paematrixformat.html |
| 26-Aug-2024 18:42:19 | overview: html/features/overview.html |
| 26-Aug-2024 18:42:19 | 0 invalid map urls |
| 26-Aug-2024 18:42:19 | 0 invalid image attributes |
| 26-Aug-2024 18:42:19 | 482 internal href links (106 with anchors) |
| 26-Aug-2024 18:42:19 | 0 invalid internal href links |
| 26-Aug-2024 18:42:19 | 0 invalid internal anchor links |
| 26-Aug-2024 18:42:19 | 111 external href links |
| 26-Aug-2024 18:42:19 | External links not verified as internet not available |
| 26-Aug-2024 18:42:19 | *** Success *** |
| 26-Aug-2024 18:42:20 | |
| 26-Aug-2024 18:42:20 | > Task :jar |
| 26-Aug-2024 18:42:20 | > Task :syncJars |
| 26-Aug-2024 18:42:20 | > Task :makeDist |
| 26-Aug-2024 18:42:20 | > Task :getdownWebsiteBuild |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | > Task :getdownDigest |
| 26-Aug-2024 18:42:22 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 26-Aug-2024 18:42:22 | 2024/08/26 18:42:21:070 WARNING Starting without install4j classes |
| 26-Aug-2024 18:42:22 | 2024/08/26 18:42:21:609 WARNING Starting without install4j classes |
| 26-Aug-2024 18:42:22 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | > Task :getdown |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. |
| 26-Aug-2024 18:42:22 | Please consult deprecation warnings for more details. |
| 26-Aug-2024 18:42:22 | |
| 26-Aug-2024 18:42:22 | BUILD SUCCESSFUL in 15s |
| 26-Aug-2024 18:42:22 | 21 actionable tasks: 21 executed |
| 26-Aug-2024 18:42:22 | Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success |
| 26-Aug-2024 18:42:22 | Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' |
| 26-Aug-2024 18:42:22 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 - Default Job #2 (JB-GDL13-JOB1-2)' ... running command line: /srv/bamboo/bamboo-home/temp/JB-GDL13-JOB1-2-ScriptBuildTask-1696571139556570805.sh ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_dependency_parent_0=JB-GDB609-2 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_dependency_parent_total=1 bamboo_planRepository_1_branchDisplayName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_repository_revision_number=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL13-JOB1-2 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL13-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDL13-JOB1 bamboo_shortPlanName=features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_name=Jalview Git bamboo_buildNumber=2 bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46498017_git_username= bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL13-JOB1-2 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_shortPlanKey=GDL13 bamboo_repository_46498017_previous_revision_number=86c07a2d67f86f9b66f0c1029e3fbe3004b37d89 bamboo_shortJobKey=JOB1 bamboo_repository_46498017_name=Jalview Git bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_buildTimeStamp=2024-08-26T18:41:14.940+01:00 bamboo_repository_previous_revision_number=86c07a2d67f86f9b66f0c1029e3fbe3004b37d89 bamboo_repository_git_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_buildResultKey=JB-GDL13-JOB1-2 bamboo_repository_branch_name=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - features-JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_46498017_revision_number=0a00266f602cde16fddd1b297279cf9b2c13a708 bamboo_repository_name=Jalview Git bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL13 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_repository_46498017_git_branch=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_branchDisplayName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 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-46301633 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 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_46498017_branch_name=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 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-GDL13-JOB1 bamboo_planKey=JB-GDL13 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498017_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_1_branchName=features/JAL-3982_JAL-3860_mouseover_genome_to_3dstructure_for_2_11_4 |
| 26-Aug-2024 18:42:22 | Finished task 'Copy JVL file and produce link in HTML' with result: Success |
| 26-Aug-2024 18:42:22 | Running post build plugin 'NCover Results Collector' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Artifact Copier' |
| 26-Aug-2024 18:42:22 | Publishing an artifact: getdown |
| 26-Aug-2024 18:42:22 | Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 197.3 ms |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Artifactory Release Management Staging' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Artifactory Build Info Copier' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'npm Cache Cleanup' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Clover Results Collector' |
| 26-Aug-2024 18:42:22 | Running post build plugin 'Docker Container Cleanup' |
| 26-Aug-2024 18:42:22 | Finalising the build... |
| 26-Aug-2024 18:42:22 | Stopping timer. |
| 26-Aug-2024 18:42:22 | Build JB-GDL13-JOB1-2 completed. |
| 26-Aug-2024 18:42:22 | Running on server: post build plugin 'NCover Results Collector' |
| 26-Aug-2024 18:42:22 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 26-Aug-2024 18:42:22 | Running on server: post build plugin 'Clover Delta Calculator' |
| 26-Aug-2024 18:42:22 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 26-Aug-2024 18:42:22 | All post build plugins have finished |
| 26-Aug-2024 18:42:22 | Generating build results summary... |
| 26-Aug-2024 18:42:22 | Saving build results to disk... |
| 26-Aug-2024 18:42:22 | Logging substituted variables... |
| 26-Aug-2024 18:42:22 | Indexing build results... |
| 26-Aug-2024 18:42:22 | Finished building JB-GDL13-JOB1-2. |