16/07/2020 6:00:01.82 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 99511 100 99511 0 0 99511 0 0:00:01 --:--:-- 0:00:01 207k 16/07/2020 6:00:02.89 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 ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_regression will be downloaded. ******************************************************************************* ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_examples will be downloaded. ******************************************************************************* Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=phenix --install_conda --python=27 ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Running in modules: create remote temporary archive builder@cci.lbl.gov:qoyqe2_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:qoyqe2_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 Existing non-git directory -- don't know what to do. skipping: scons ===== Running in modules: create remote temporary archive builder@cci.lbl.gov:wnbh_a_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:wnbh_a_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 builder@cci.lbl.gov:ilp7_t_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:ilp7_t_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 3812ecd3e..d064f022f master -> origin/master + 94992091d...06aa88364 azure -> origin/azure (forced update) c7cb34842..3e1c5fddd not-params -> origin/not-params b4bb2fac7..714147151 template_image_range -> origin/template_image_range Updating 3812ecd3e..d064f022f Fast-forward .azure-pipelines/azure-pipelines-linux.yml | 1 + .travis.yml | 67 +- .travis/python2-supported-files | 648 ---------------- .travis/run-flake8 | 19 - .travis/setup-base | 30 - .travis/setup-base3 | 2 +- __init__.py | 2 +- algorithms/scaling/scale_and_filter.py | 4 +- algorithms/statistics/cc_half_algorithm.py | 7 +- algorithms/symmetry/__init__.py | 23 +- algorithms/symmetry/absences/screw_axes.py | 6 +- command_line/damage_analysis.py | 20 +- command_line/estimate_resolution.py | 124 +++ command_line/generate_tutorial_text.py | 6 +- command_line/refine_error_model.py | 6 +- command_line/resolutionizer.py | 82 -- conftest.py | 25 - newsfragments/1330.feature | 1 + pychef/__init__.py | 13 +- report/plots.py | 218 +++--- report/test_plots.py | 8 +- templates/delta_cc_half_report.html | 13 - templates/error_model_report.html | 13 - templates/macros.html | 4 +- ...age_analysis_report.html => simple_report.html} | 2 +- templates/systematic_absences_report.html | 15 - test/command_line/test_compute_delta_cchalf.py | 4 +- test/command_line/test_estimate_resolution.py | 94 +++ test/python3/test_skipping.py | 5 - test/python3/test_syntaxerror_on_import.py | 7 - util/resolution_analysis.py | 671 ++++++++++++++++ util/resolutionizer.py | 856 --------------------- util/test_resolution_analysis.py | 111 +++ util/test_resolutionizer.py | 82 -- 34 files changed, 1198 insertions(+), 1991 deletions(-) delete mode 100644 .travis/python2-supported-files delete mode 100755 .travis/run-flake8 delete mode 100755 .travis/setup-base create mode 100644 command_line/estimate_resolution.py delete mode 100644 command_line/resolutionizer.py create mode 100644 newsfragments/1330.feature delete mode 100644 templates/delta_cc_half_report.html delete mode 100644 templates/error_model_report.html rename templates/{damage_analysis_report.html => simple_report.html} (70%) delete mode 100644 templates/systematic_absences_report.html create mode 100644 test/command_line/test_estimate_resolution.py delete mode 100644 test/python3/test_skipping.py delete mode 100644 test/python3/test_syntaxerror_on_import.py create mode 100644 util/resolution_analysis.py delete mode 100644 util/resolutionizer.py create mode 100644 util/test_resolution_analysis.py delete mode 100644 util/test_resolutionizer.py Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 73a1a95..30d8a13 master -> origin/master * [new branch] masked-bandit -> origin/masked-bandit * [new branch] move-result -> origin/move-result Updating 73a1a95..30d8a13 Fast-forward command_line/radial_average.py | 83 ++++++++++++++++++++++++++++++++++++------ 1 file changed, 71 insertions(+), 12 deletions(-) Current branch master is up to date. Already up to date. Current branch master is up to date. Updating 'ccp4io_adaptbx': At revision 143. There is no tracking information for the current branch. Please specify which branch you want to rebase against. See git-pull(1) for details. git pull If you wish to set tracking information for this branch you can do so with: git branch --set-upstream-to=origin/ master ===== 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\amber_library: git pull --rebase ===== Running in modules: svn update ccp4io_adaptbx --non-interactive --trust-server-cert ===== Running in modules\solve_resolve: git pull --rebase Process failed with return code 1