07/06/2019 6:00:01.50 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 90301 100 90301 0 0 90301 0 0:00:01 --:--:-- 0:00:01 235k 07/06/2019 6:00:02.16 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:ixyxqt_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:ixyxqt_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:s7axri_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:s7axri_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:iglcef_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:iglcef_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:rwn6jy_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:rwn6jy_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.link/repo/dials/dependencies/dials-1.13/msgpack-3.1.1.tar.gz: 484 kB From https://github.com/dials/dials 0d9ed724f..8718ebd81 master -> origin/master + 9d80920bb...e38f3dd55 index-refactor -> origin/index-refactor (forced update) Updating 0d9ed724f..8718ebd81 Fast-forward .flake8 | 7 ++ algorithms/scaling/active_parameter_managers.py | 7 +- .../scaling/cross_validation/cross_validate.py | 9 +- .../cross_validation/test_crossvalidation.py | 11 ++- algorithms/scaling/error_model/error_model.py | 3 +- algorithms/scaling/outlier_rejection.py | 15 +--- algorithms/scaling/scaler_factory.py | 8 +- algorithms/scaling/scaling_library.py | 45 +--------- algorithms/scaling/test_error_model.py | 3 +- algorithms/scaling/test_outlier_rejection.py | 5 +- algorithms/scaling/test_param_manager.py | 5 +- algorithms/scaling/test_scaler_factory.py | 4 +- algorithms/scaling/test_weighting.py | 3 +- algorithms/scaling/weighting.py | 3 +- command_line/assign_experiment_identifiers.py | 68 +++++++++------ command_line/cosym.py | 12 ++- command_line/export.py | 96 +++++++++++++++------- command_line/reciprocal_lattice_viewer.py | 7 +- command_line/rl_png.py | 43 ++++------ command_line/scale.py | 66 ++++++++++++--- command_line/symmetry.py | 26 +++--- precommitbx/installer.py | 57 ++++++++++++- test/array_family/test_reflection_table.py | 15 +--- test/util/test_exclude_images.py | 7 +- test/util/test_multi_dataset_handling.py | 46 +++++------ util/exclude_images.py | 5 +- util/export_json.py | 4 +- util/export_mtz.py | 10 +-- util/export_sadabs.py | 14 ++-- util/export_xds_ascii.py | 11 +-- util/multi_dataset_handling.py | 60 +++++++------- util/options.py | 3 +- 32 files changed, 381 insertions(+), 297 deletions(-) create mode 100644 .flake8 Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx b21bf4c..ed81e0f master -> origin/master da8034f..495bef7 format-registration -> origin/format-registration Updating b21bf4c..ed81e0f Fast-forward tests/serialize/test_filename.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) 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': At revision 4630. Updating 'opt_resources': At revision 6. Updating 'phenix': At revision 12941. 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. Already up to date. Current branch master is up to date. Updating 'chem_data': Fetching external item into 'chem_data\geostd': External at revision 202. 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 1327. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Updating 'amber_adaptbx': At revision 365. 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