23/06/2020 6:00:01.74 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 99218 100 99218 0 0 99218 0 0:00:01 --:--:-- 0:00:01 295k 23/06/2020 6:00:02.61 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:gyfhos_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:gyfhos_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:kkoxdh_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:kkoxdh_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:wfim1n_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:wfim1n_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 903e73ccb..0bba3ff75 master -> origin/master cd48176d0..1876da517 dials-next -> origin/dials-next 161343c10..99b5f3ec3 masked_refl_profile_fitting -> origin/masked_refl_profile_fitting * [new branch] remove-read-anything-function -> origin/remove-read-anything-function 0ef01b1be..8f9b597f4 scale-when-stacking -> origin/scale-when-stacking dade4963c..64361f6c7 scaling_intensity_handling -> origin/scaling_intensity_handling Updating 903e73ccb..0bba3ff75 Fast-forward .conda-envs/linux.txt | 1 + .conda-envs/macos.txt | 1 + .travis/python2-supported-files | 1 - algorithms/integration/parallel_integrator.py | 7 +- algorithms/integration/processor.py | 2 +- algorithms/scaling/algorithm.py | 10 +- algorithms/scaling/boost_python/scaling_ext.cc | 2 + algorithms/scaling/boost_python/scaling_helper.cc | 6 + algorithms/scaling/combine_intensities.py | 86 ++++----- algorithms/scaling/outlier_rejection.py | 113 ++++++------ algorithms/scaling/scaler_factory.py | 26 ++- algorithms/scaling/scaling_helper.h | 25 +++ algorithms/scaling/scaling_library.py | 89 +++++----- algorithms/scaling/test_combine_intensities.py | 21 +++ algorithms/scaling/test_outlier_rejection.py | 49 +++++ algorithms/scaling/test_scale.py | 10 +- algorithms/scaling/test_scaler_factory.py | 49 ++++- algorithms/scaling/test_scaling_library.py | 13 +- command_line/detect_blanks.py | 197 ++------------------- command_line/refine_error_model.py | 4 +- installer/bootstrap.py | 1 - model/serialize/load.py | 3 +- newsfragments/1288.misc | 2 + newsfragments/1300.bugfix | 1 + .../reflection_basis/test_beam_vector_map.py | 5 +- .../reflection_basis/test_grid_index_generator.py | 12 +- .../algorithms/reflection_basis/test_map_frames.py | 34 ++-- test/algorithms/reflection_basis/test_transform.py | 6 +- test/algorithms/shoebox/test_bbox_calculator.py | 13 +- test/command_line/test_detect_blanks.py | 83 +++++++++ test/util/test_filter_reflections_export.py | 2 + util/detect_blanks.py | 165 +++++++++++++++++ util/filter_reflections.py | 76 +++++++- util/test_detect_blanks.py | 129 ++++++++++++++ 34 files changed, 830 insertions(+), 414 deletions(-) create mode 100644 newsfragments/1288.misc create mode 100644 newsfragments/1300.bugfix create mode 100644 test/command_line/test_detect_blanks.py create mode 100644 util/detect_blanks.py create mode 100644 util/test_detect_blanks.py Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx be08057..b0d1792 master -> origin/master 6d28c24..3fa983a dls-eiger-0xffff -> origin/dls-eiger-0xffff * [new branch] eiger-borken-links -> origin/eiger-borken-links Updating be08057..b0d1792 Fast-forward format/FormatCBFMiniPilatus.py | 145 +++++++++++++++- format/FormatCBFMiniPilatusDLS6MSN100.py | 274 ------------------------------ format/FormatCBFMiniPilatusDLS6MSN126.py | 272 ----------------------------- format/nexus.py | 5 +- newsfragments/177.feature | 1 + tests/format/test_FormatCBFMiniPilatus.py | 47 +++++ 6 files changed, 191 insertions(+), 553 deletions(-) create mode 100644 newsfragments/177.feature create mode 100644 tests/format/test_FormatCBFMiniPilatus.py 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