simple	29-Jun-2026 15:53:14	Build Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests #1 (JB-GDB757-JOB1-1) started building on agent Default Agent
simple	29-Jun-2026 15:53:14	
simple	29-Jun-2026 15:53:14	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1
simple	29-Jun-2026 15:53:14	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests #1 (JB-GDB757-JOB1-1)
simple	29-Jun-2026 15:53:14	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	29-Jun-2026 15:53:14	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1
simple	29-Jun-2026 15:53:14	Updating source code to revision: 479f0f17b7b8a7e9a89d505f560568c0947da9eb
simple	29-Jun-2026 15:53:14	Fetching 'refs/heads/patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	29-Jun-2026 15:53:14	Checking out revision 479f0f17b7b8a7e9a89d505f560568c0947da9eb.
simple	29-Jun-2026 15:53:14	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1/.git'.
simple	29-Jun-2026 15:53:14	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1'...
simple	29-Jun-2026 15:53:14	done.
simple	29-Jun-2026 15:53:17	error: unable to write file appletlib.zip
simple	29-Jun-2026 15:53:17	fatal: cannot create directory at 'appletlib': No space left on device
error	29-Jun-2026 15:53:18	Checkout to revision 479f0f17b7b8a7e9a89d505f560568c0947da9eb has failed.
simple	29-Jun-2026 15:53:18	Warning: failed to checkout source code to directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1', trying to recover...
simple	29-Jun-2026 15:53:18	Cleaned source directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1'...
simple	29-Jun-2026 15:53:18	Checking out revision 479f0f17b7b8a7e9a89d505f560568c0947da9eb.
simple	29-Jun-2026 15:53:18	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1/.git'.
simple	29-Jun-2026 15:53:18	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1'...
simple	29-Jun-2026 15:53:18	done.
simple	29-Jun-2026 15:53:20	error: unable to write file appletlib.zip
simple	29-Jun-2026 15:53:20	fatal: cannot create directory at 'appletlib': No space left on device
error	29-Jun-2026 15:53:20	Checkout to revision 479f0f17b7b8a7e9a89d505f560568c0947da9eb has failed.
simple	29-Jun-2026 15:53:20	Updating source code to revision: 479f0f17b7b8a7e9a89d505f560568c0947da9eb
simple	29-Jun-2026 15:53:20	Fetching 'refs/heads/patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail' from 'https://gitlab.jalview.org/jalview/jalview.git'.
error	29-Jun-2026 15:53:20	Cannot fetch branch 'refs/heads/patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail' from 'https://gitlab.jalview.org/jalview/jalview.git' to source directory '/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0'. fatal: FETCH_HEAD is empty after fetch.
simple	29-Jun-2026 15:53:20	Warning: failed to retrieve source code to cache directory '/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0', trying to recover...
simple	29-Jun-2026 15:53:20	Cleaned cache directory '/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0', trying to fetch the code once again...
simple	29-Jun-2026 15:53:20	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0/.git'.
simple	29-Jun-2026 15:53:20	Initialized empty Git repository in /srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0/.git/
simple	29-Jun-2026 15:53:20	Fetching 'refs/heads/patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	29-Jun-2026 15:54:27	From https://gitlab.jalview.org/jalview/jalview
simple	29-Jun-2026 15:54:27	 * [new branch]      patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail -> patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail
simple	29-Jun-2026 15:54:28	From https://gitlab.jalview.org/jalview/jalview
simple	29-Jun-2026 15:54:28	 * [new tag]         Develop-2_11_2_0-d20201215 -> Develop-2_11_2_0-d20201215
simple	29-Jun-2026 15:54:28	 * [new tag]         Develop-2_11_2_0-d20210205 -> Develop-2_11_2_0-d20210205
simple	29-Jun-2026 15:54:28	 * [new tag]         Jalview_2_9 -> Jalview_2_9
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_0 -> Release_2_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_01 -> Release_2_01
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_02 -> Release_2_02
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_03 -> Release_2_03
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_04 -> Release_2_04
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_05 -> Release_2_05
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_05b -> Release_2_05b
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_06 -> Release_2_06
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_1 -> Release_2_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_0 -> Release_2_10_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_0b1 -> Release_2_10_0b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_0b1_final -> Release_2_10_0b1_final
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_0b1_sourcepub -> Release_2_10_0b1_sourcepub
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_2 -> Release_2_10_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_2b1 -> Release_2_10_2b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_2b2 -> Release_2_10_2b2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_3 -> Release_2_10_3
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_3b1 -> Release_2_10_3b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_4 -> Release_2_10_4
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_4b1 -> Release_2_10_4b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_10_5 -> Release_2_10_5
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_0 -> Release_2_11_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_0 -> Release_2_11_1_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_1 -> Release_2_11_1_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_2 -> Release_2_11_1_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_3 -> Release_2_11_1_3
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_4 -> Release_2_11_1_4
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_5 -> Release_2_11_1_5
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_6 -> Release_2_11_1_6
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_1_7 -> Release_2_11_1_7
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_0 -> Release_2_11_2_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_1 -> Release_2_11_2_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_2 -> Release_2_11_2_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_3 -> Release_2_11_2_3
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_4 -> Release_2_11_2_4
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_5 -> Release_2_11_2_5
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_2_6 -> Release_2_11_2_6
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_3_0 -> Release_2_11_3_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_3_1 -> Release_2_11_3_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_3_2 -> Release_2_11_3_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_3_3 -> Release_2_11_3_3
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_5_0 -> Release_2_11_5_0
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_11_5_1 -> Release_2_11_5_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_2 -> Release_2_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_3 -> Release_2_3
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_3_buildfix -> Release_2_3_buildfix
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_4 -> Release_2_4
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_5 -> Release_2_5
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_5_branch -> Release_2_5_branch
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_7 -> Release_2_7
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_8 -> Release_2_8
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_8_0b1 -> Release_2_8_0b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_8_1 -> Release_2_8_1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_8_2 -> Release_2_8_2
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_8_2b1 -> Release_2_8_2b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_9_0b1 -> Release_2_9_0b1
simple	29-Jun-2026 15:54:28	 * [new tag]         Release_2_9_0b2 -> Release_2_9_0b2
simple	29-Jun-2026 15:54:28	 * [new tag]         Root_Release_2_5_Branch -> Root_Release_2_5_Branch
simple	29-Jun-2026 15:54:28	 * [new tag]         Root_VamJalview_2_07b+ -> Root_VamJalview_2_07b+
simple	29-Jun-2026 15:54:28	 * [new tag]         start      -> start
simple	29-Jun-2026 15:54:28	Fetching to cache directory '/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0' completed, proceeding with checkout...
simple	29-Jun-2026 15:54:28	Checking out revision 479f0f17b7b8a7e9a89d505f560568c0947da9eb.
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/main does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4672_for_2115_pdbe_query does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/main does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4672_for_2115_pdbe_query does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/main does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4672_for_2115_pdbe_query does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/main does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4672_for_2115_pdbe_query does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/main does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4410_multimers_from_3dbeacons does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/patch/JAL-4672_for_2115_pdbe_query does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	29-Jun-2026 15:54:28	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	29-Jun-2026 15:54:31	Switched to a new branch 'patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail'
simple	29-Jun-2026 15:54:31	Branch patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail set up to track remote branch patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail from origin.
simple	29-Jun-2026 15:54:31	Updated source code to revision: 479f0f17b7b8a7e9a89d505f560568c0947da9eb
simple	29-Jun-2026 15:54:31	Finished task 'Checkout Default Repository' with result: Success
simple	29-Jun-2026 15:54:31	Running pre-build action: VCS Version Collector
simple	29-Jun-2026 15:54:31	Running pre-build action: Artifactory Release Staging
simple	29-Jun-2026 15:54:31	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	29-Jun-2026 15:54:31	Bamboo Artifactory Plugin version: 2.6.2
command	29-Jun-2026 15:54:31	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests #1 (JB-GDB757-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_repository_revision_number=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB757-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169088_branch_name=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildKey=JB-GDB757-JOB1\nbamboo_shortPlanName=patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB757-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_shortPlanKey=GDB757\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_buildTimeStamp=2026-06-29T15:53:14.331+01:00\nbamboo_repository_git_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildResultKey=JB-GDB757-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_48169088_revision_number=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_planRepository_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972607\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169088_git_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\nbamboo_repository_48169088_name=Jalview Gitlab\nbamboo_planKey=JB-GDB757\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_48169088_git_username=\nbamboo_repository_48169088_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	29-Jun-2026 15:54:31	2414
build	29-Jun-2026 15:54:32	Starting a Gradle Daemon (subsequent builds will be faster)
error	29-Jun-2026 15:54:36	
error	29-Jun-2026 15:54:36	FAILURE: Build failed with an exception.
error	29-Jun-2026 15:54:36	
error	29-Jun-2026 15:54:36	* What went wrong:
error	29-Jun-2026 15:54:36	Could not resolve all files for configuration 'classpath'.
error	29-Jun-2026 15:54:36	> Could not resolve org.gradle.toolchains:foojay-resolver:1.0.0.
error	29-Jun-2026 15:54:36	  Required by:
error	29-Jun-2026 15:54:36	      unspecified:unspecified:unspecified > org.gradle.toolchains.foojay-resolver-convention:org.gradle.toolchains.foojay-resolver-convention.gradle.plugin:1.0.0
error	29-Jun-2026 15:54:36	   > No matching variant of org.gradle.toolchains:foojay-resolver:1.0.0 was found. The consumer was configured to find a runtime of a library compatible with Java 11, packaged as a jar, and its dependencies declared externally, as well as attribute 'org.gradle.plugin.api-version' with value '7.4.2' but:
error	29-Jun-2026 15:54:36	       - Variant 'javadocElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a component, and its dependencies declared externally:
error	29-Jun-2026 15:54:36	           - Incompatible because this component declares documentation and the consumer needed a library
error	29-Jun-2026 15:54:36	           - Other compatible attributes:
error	29-Jun-2026 15:54:36	               - Doesn't say anything about its target Java version (required compatibility with Java 11)
error	29-Jun-2026 15:54:36	               - Doesn't say anything about its elements (required them packaged as a jar)
error	29-Jun-2026 15:54:36	               - Doesn't say anything about org.gradle.plugin.api-version (required '7.4.2')
error	29-Jun-2026 15:54:36	       - Variant 'shadowRuntimeElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a library, packaged as a jar, and its dependencies repackaged (shadow jar):
error	29-Jun-2026 15:54:36	           - Incompatible because this component declares a component compatible with Java 17, as well as attribute 'org.gradle.plugin.api-version' with value '7.6' and the consumer needed a component compatible with Java 11, as well as attribute 'org.gradle.plugin.api-version' with value '7.4.2'
error	29-Jun-2026 15:54:36	       - Variant 'sourcesElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a component, and its dependencies declared externally:
error	29-Jun-2026 15:54:36	           - Incompatible because this component declares documentation and the consumer needed a library
error	29-Jun-2026 15:54:36	           - Other compatible attributes:
error	29-Jun-2026 15:54:36	               - Doesn't say anything about its target Java version (required compatibility with Java 11)
error	29-Jun-2026 15:54:36	               - Doesn't say anything about its elements (required them packaged as a jar)
error	29-Jun-2026 15:54:36	               - Doesn't say anything about org.gradle.plugin.api-version (required '7.4.2')
error	29-Jun-2026 15:54:36	
error	29-Jun-2026 15:54:36	* Try:
error	29-Jun-2026 15:54:36	> Run with --stacktrace option to get the stack trace.
error	29-Jun-2026 15:54:36	> Run with --info or --debug option to get more log output.
error	29-Jun-2026 15:54:36	> Run with --scan to get full insights.
error	29-Jun-2026 15:54:36	
error	29-Jun-2026 15:54:36	* Get more help at https://help.gradle.org
error	29-Jun-2026 15:54:36	
error	29-Jun-2026 15:54:36	BUILD FAILED in 4s
simple	29-Jun-2026 15:54:36	
simple	29-Jun-2026 15:54:36	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
simple	29-Jun-2026 15:54:36	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	29-Jun-2026 15:54:36	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	29-Jun-2026 15:54:36	Bamboo Artifactory Plugin version: 2.6.2
command	29-Jun-2026 15:54:36	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests #1 (JB-GDB757-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_repository_revision_number=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB757-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169088_branch_name=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildKey=JB-GDB757-JOB1\nbamboo_shortPlanName=patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB757-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_shortPlanKey=GDB757\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_buildTimeStamp=2026-06-29T15:53:14.331+01:00\nbamboo_repository_git_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildResultKey=JB-GDB757-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4320_JAL-4671_fix_hidpi_mockitofail - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_48169088_revision_number=479f0f17b7b8a7e9a89d505f560568c0947da9eb\nbamboo_planRepository_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972607\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169088_git_branch=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1\nbamboo_repository_48169088_name=Jalview Gitlab\nbamboo_planKey=JB-GDB757\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_48169088_git_username=\nbamboo_repository_48169088_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4320_JAL-4671_fix_hidpi_mockitofail\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	29-Jun-2026 15:54:36	2414
error	29-Jun-2026 15:54:39	
error	29-Jun-2026 15:54:39	FAILURE: Build failed with an exception.
error	29-Jun-2026 15:54:39	
error	29-Jun-2026 15:54:39	* What went wrong:
error	29-Jun-2026 15:54:39	Could not resolve all files for configuration 'classpath'.
error	29-Jun-2026 15:54:39	> Could not resolve org.gradle.toolchains:foojay-resolver:1.0.0.
error	29-Jun-2026 15:54:39	  Required by:
error	29-Jun-2026 15:54:39	      unspecified:unspecified:unspecified > org.gradle.toolchains.foojay-resolver-convention:org.gradle.toolchains.foojay-resolver-convention.gradle.plugin:1.0.0
error	29-Jun-2026 15:54:39	   > No matching variant of org.gradle.toolchains:foojay-resolver:1.0.0 was found. The consumer was configured to find a runtime of a library compatible with Java 11, packaged as a jar, and its dependencies declared externally, as well as attribute 'org.gradle.plugin.api-version' with value '7.4.2' but:
error	29-Jun-2026 15:54:39	       - Variant 'javadocElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a component, and its dependencies declared externally:
error	29-Jun-2026 15:54:39	           - Incompatible because this component declares documentation and the consumer needed a library
error	29-Jun-2026 15:54:39	           - Other compatible attributes:
error	29-Jun-2026 15:54:39	               - Doesn't say anything about its target Java version (required compatibility with Java 11)
error	29-Jun-2026 15:54:39	               - Doesn't say anything about its elements (required them packaged as a jar)
error	29-Jun-2026 15:54:39	               - Doesn't say anything about org.gradle.plugin.api-version (required '7.4.2')
error	29-Jun-2026 15:54:39	       - Variant 'shadowRuntimeElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a library, packaged as a jar, and its dependencies repackaged (shadow jar):
error	29-Jun-2026 15:54:39	           - Incompatible because this component declares a component compatible with Java 17, as well as attribute 'org.gradle.plugin.api-version' with value '7.6' and the consumer needed a component compatible with Java 11, as well as attribute 'org.gradle.plugin.api-version' with value '7.4.2'
error	29-Jun-2026 15:54:39	       - Variant 'sourcesElements' capability org.gradle.toolchains:foojay-resolver:1.0.0 declares a runtime of a component, and its dependencies declared externally:
error	29-Jun-2026 15:54:39	           - Incompatible because this component declares documentation and the consumer needed a library
error	29-Jun-2026 15:54:39	           - Other compatible attributes:
error	29-Jun-2026 15:54:39	               - Doesn't say anything about its target Java version (required compatibility with Java 11)
error	29-Jun-2026 15:54:39	               - Doesn't say anything about its elements (required them packaged as a jar)
error	29-Jun-2026 15:54:39	               - Doesn't say anything about org.gradle.plugin.api-version (required '7.4.2')
error	29-Jun-2026 15:54:39	
error	29-Jun-2026 15:54:39	* Try:
error	29-Jun-2026 15:54:39	> Run with --stacktrace option to get the stack trace.
error	29-Jun-2026 15:54:39	> Run with --info or --debug option to get more log output.
error	29-Jun-2026 15:54:39	> Run with --scan to get full insights.
error	29-Jun-2026 15:54:39	
error	29-Jun-2026 15:54:39	* Get more help at https://help.gradle.org
error	29-Jun-2026 15:54:39	
error	29-Jun-2026 15:54:39	BUILD FAILED in 2s
simple	29-Jun-2026 15:54:40	
simple	29-Jun-2026 15:54:40	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport] was 1 while expected 0
simple	29-Jun-2026 15:54:40	Finished task 'Clover Report' with result: Failed
simple	29-Jun-2026 15:54:40	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	29-Jun-2026 15:54:40	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1...
simple	29-Jun-2026 15:54:40	Failing task since test cases were expected but none were found.
simple	29-Jun-2026 15:54:40	Finished task 'TestNG Parser' with result: Failed
simple	29-Jun-2026 15:54:40	Running post build plugin 'NCover Results Collector'
simple	29-Jun-2026 15:54:40	Running post build plugin 'Artifact Copier'
simple	29-Jun-2026 15:54:40	Publishing an artifact: Clover Report (System)
error	29-Jun-2026 15:54:40	Unable to publish artifact [Clover Report (System)]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1/build/reports/clover does not exist.
simple	29-Jun-2026 15:54:40	The artifact hasn't been successfully published after 363.1 μs
simple	29-Jun-2026 15:54:40	Publishing an artifact: TestNG report
error	29-Jun-2026 15:54:40	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1/build/reports/tests/test does not exist.
simple	29-Jun-2026 15:54:40	The artifact hasn't been successfully published after 55.82 μs
simple	29-Jun-2026 15:54:40	Running post build plugin 'Artifactory Release Management Staging'
simple	29-Jun-2026 15:54:40	Running post build plugin 'Artifactory Build Info Copier'
simple	29-Jun-2026 15:54:40	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	29-Jun-2026 15:54:40	Running post build plugin 'npm Cache Cleanup'
simple	29-Jun-2026 15:54:40	Running post build plugin 'Clover Results Collector'
error	29-Jun-2026 15:54:40	Failed to execute plugin 'Clover Results Collector' with error: No file matches the specified pattern:build/reports/clover/clover.xml in [/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB757-JOB1]
simple	29-Jun-2026 15:54:40	Running post build plugin 'Docker Container Cleanup'
simple	29-Jun-2026 15:54:40	Finalising the build...
simple	29-Jun-2026 15:54:40	Stopping timer.
simple	29-Jun-2026 15:54:40	Build JB-GDB757-JOB1-1 completed.
simple	29-Jun-2026 15:54:40	Running on server: post build plugin 'NCover Results Collector'
simple	29-Jun-2026 15:54:40	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	29-Jun-2026 15:54:40	Running on server: post build plugin 'Clover Delta Calculator'
simple	29-Jun-2026 15:54:40	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	29-Jun-2026 15:54:40	All post build plugins have finished
simple	29-Jun-2026 15:54:40	Generating build results summary...
simple	29-Jun-2026 15:54:40	Saving build results to disk...
simple	29-Jun-2026 15:54:40	Logging substituted variables...
simple	29-Jun-2026 15:54:40	Indexing build results...
simple	29-Jun-2026 15:54:40	Finished building JB-GDB757-JOB1-1.