11/06/2019 6:00:01.58 Get bootstrap.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 90300 100 90300 0 0 90300 0 0:00:01 --:--:-- 0:00:01 296k 11/06/2019 6:00:02.22 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base_tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q base_tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty build /MIR /COPYALL 1>nul ) & rmdir /S /Q build\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty conda_base /MIR /COPYALL 1>nul ) & rmdir /S /Q conda_base\ & ) The system cannot find the file specified. Performing actions: cleanup hot update base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_base_packages.py --python-shared --all --phenix --labelit --dials --xia2 --nproc=20 --skip-if-exists ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:pfzgz6_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:pfzgz6_annlib.tar.gz ===== Running in modules: delete remote temporary archive of annlib ===== Running in modules: extracting archive files to annlib ===== Running in modules: delete local temporary archive of annlib ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:fvae0f_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:fvae0f_scons.tar.gz ===== Running in modules: delete remote temporary archive of scons ===== Running in modules: extracting archive files to scons ===== Running in modules: delete local temporary archive of scons ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:jupzvy_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:jupzvy_ccp4io.tar.gz ===== Running in modules: delete remote temporary archive of ccp4io ===== Running in modules: extracting archive files to ccp4io ===== Running in modules: delete local temporary archive of ccp4io ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:0t1hru_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:0t1hru_eigen.tar.gz ===== Running in modules: delete remote temporary archive of eigen ===== Running in modules: extracting archive files to eigen ===== Running in modules: delete local temporary archive of eigen ===== Downloading https://gitcdn.xyz/repo/dials/dependencies/dials-1.13/msgpack-3.1.1.tar.gz: 484 kB From https://github.com/dials/dials 72e3083b7..2b430ef41 master -> origin/master * [new branch] revert-800-pia-matplotlib-fix -> origin/revert-800-pia-matplotlib-fix Updating 72e3083b7..2b430ef41 Fast-forward algorithms/spot_finding/per_image_analysis.py | 111 ++-- array_family/flex.py | 24 +- command_line/analyse_output.py | 163 ++--- command_line/cosym.py | 87 +-- command_line/export.py | 24 +- command_line/filter_reflections.py | 727 ++++++++++----------- command_line/reindex.py | 23 +- command_line/spot_counts_per_image.py | 4 + command_line/symmetry.py | 83 +-- conftest.py | 14 - .../algorithms/dials.algorithms.indexing.rst | 12 +- libtbx_config | 2 +- newsfragments/795.misc | 1 + pytest.ini | 4 + test/command_line/test_combine_experiments.py | 4 +- test/command_line/test_filter_reflections.py | 41 +- test/util/test_filter_reflections_export.py | 95 ++- util/export_json.py | 39 +- util/export_mtz.py | 2 - util/filter_reflections.py | 518 ++++++++------- 20 files changed, 932 insertions(+), 1046 deletions(-) create mode 100644 newsfragments/795.misc Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 70ee2c5..ab2a81a master -> origin/master * [new branch] d-d -> origin/d-d Updating 70ee2c5..ab2a81a Fast-forward conftest.py | 22 +++++++++++----------- tests/format/test_FormatHDF5EigerNearlyNexus.py | 2 ++ tests/format/test_FormatNexus.py | 2 ++ tests/format/test_FormatNexusEigerDLS16MI04.py | 1 + tests/model/test_experiment_list.py | 1 + tests/test_image_readers.py | 3 ++- tests/test_imageset.py | 2 ++ tests/test_regression_images.py | 15 ++++++++++----- tests/test_split_singleimage_datablock.py | 2 ++ 9 files changed, 33 insertions(+), 17 deletions(-) Current branch master is up to date. Updating 'ccp4io_adaptbx': At revision 143. Updating 'solve_resolve': At revision 1726. Updating 'clipper': At revision 19. Updating 'ksdssp': At revision 14. Updating 'phenix_regression': A phenix_regression\development\tst_rama_z_score.py Updated to revision 4633. Updating 'opt_resources': At revision 6. Updating 'phenix': U phenix\wxGUI2\Programs\__init__.params A phenix\wxGUI2\Programs\PreparePDBDeposition.py A phenix\wxGUI2\Programs\PDBValidationReport.py A phenix\wxGUI2\program_template\get_pdb_validation_report.py A phenix\wxGUI2\program_template\prepare_pdb_deposition.py U phenix\phenix\command_line\rama_z_score.py U phenix\phenix\pdb_tools\rama_z_score\rama_z_score.py U phenix\phenix\tracking\program_info.params A phenix\phenix\autosol\analyze_errors.py A phenix\phenix\autosol\randomize_map.py U phenix\phenix\programs\rama_z_score.py U phenix\phenix\programs\get_pdb_validation_report.py Updated to revision 12952. Updating 'Plex': At revision 8. Updating 'tntbx': At revision 50. Updating 'pulchra': At revision 8. Updating 'PyQuante': At revision 25. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. Updating 'suitename': At revision 11. From https://github.com/xia2/xia2 1c377b3a..4496be27 master -> origin/master Updating 1c377b3a..4496be27 Fast-forward conftest.py | 13 ------------- libtbx_config | 2 +- pyproject.toml | 3 +++ 3 files changed, 4 insertions(+), 14 deletions(-) Current branch master is up to date. Updating 'chem_data': Fetching external item into 'chem_data\geostd': U chem_data\geostd\list\geostd_list.cif Updated external to revision 203. At revision 317. X chem_data\geostd Performing status on external item at 'chem_data\geostd': Already up to date. Current branch master is up to date. warning: redirecting to https://git.uis.cam.ac.uk/cimr-phaser/phaser_regression.git/ Already up to date. Current branch master is up to date. Updating 'phenix_examples': At revision 96. Updating 'reel': At revision 265. Updating 'phenix_html': At revision 1329. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Updating 'amber_adaptbx': U amber_adaptbx\command_line\AmberPrepClass.py U amber_adaptbx\utils.py U amber_adaptbx\les_builder\build.py U amber_adaptbx\pdb4amber\pdb4amber.py U amber_adaptbx\tests\files\1aho\test_AmberPrep_LES U amber_adaptbx\tests\files\1aho\les\4phenix_1aho.pdb U amber_adaptbx\tests\files\1aho\les\addles.in U amber_adaptbx\tests\files\1aho\les\les.log U amber_adaptbx\tests\files\1aho\non-les\4phenix_1aho.pdb U amber_adaptbx\tests\files\1aho\non-les\non-les.log U amber_adaptbx\tests\files\3cfb\test_phenix.refine Updated to revision 376. Updating 'labelit': At revision 2072. Updating 'elbow': At revision 3773. Updating 'muscle': At revision 10. Updating 'gui_resources': At revision 58. python: can't open file 'modules\cctbx_project\libtbx\auto_build\install_base_packages.py': [Errno 2] No such file or directory ===== Running in modules: extracting files from msgpack-3.1.1.tar.gz ===== Running in modules\dials: git pull --rebase ===== Running in modules: svn update probe --non-interactive --trust-server-cert ===== Running in modules: svn update reduce --non-interactive --trust-server-cert ===== Running in modules\dxtbx: git pull --rebase ===== Running in modules: svn update ccp4io_adaptbx --non-interactive --trust-server-cert ===== Running in modules: svn update solve_resolve --non-interactive --trust-server-cert ===== Running in modules: svn update clipper --non-interactive --trust-server-cert ===== Running in modules: svn update ksdssp --non-interactive --trust-server-cert ===== Running in modules: svn update phenix_regression --non-interactive --trust-server-cert ===== Running in modules: svn update opt_resources --non-interactive --trust-server-cert ===== Running in modules: svn update phenix --non-interactive --trust-server-cert ===== Running in modules: svn update Plex --non-interactive --trust-server-cert ===== Running in modules: svn update tntbx --non-interactive --trust-server-cert ===== Running in modules: svn update pulchra --non-interactive --trust-server-cert ===== Running in modules: svn update PyQuante --non-interactive --trust-server-cert ===== Running in modules\boost: git pull --rebase Existing non-git directory -- don't know what to do. skipping: cctbx_project ================================================================================ CCTBX moved to git on November 22, 2016. To update cctbx_project to the last available subversion revision please run "svn update" while in the cctbx_project directory. ******************************************************************************** ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Running in modules: svn update suitename --non-interactive --trust-server-cert ===== Running in modules\xia2: git pull --rebase ===== Running in modules: svn update chem_data --non-interactive --trust-server-cert ===== Running in modules\phaser: git pull --rebase ===== Running in modules\phaser_regression: git pull --rebase ===== Running in modules: svn update phenix_examples --non-interactive --trust-server-cert ===== Running in modules: svn update reel --non-interactive --trust-server-cert ===== Running in modules: svn update phenix_html --non-interactive --trust-server-cert ===== Running in modules: svn update king --non-interactive --trust-server-cert ===== Running in modules\cbflib: git pull --rebase ===== Running in modules: svn update amber_adaptbx --non-interactive --trust-server-cert ===== Running in modules: svn update labelit --non-interactive --trust-server-cert ===== Running in modules: svn update elbow --non-interactive --trust-server-cert ===== Running in modules: svn update muscle --non-interactive --trust-server-cert ===== Running in modules: svn update gui_resources --non-interactive --trust-server-cert removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules, walk? True removed 0 files ===== Running in .: base Process failed with return code 2