10/04/2020 6:00:02.31 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 93605 100 93605 0 0 93605 0 0:00:01 --:--:-- 0:00:01 208k 10/04/2020 6:00:02.99 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 builder@cci.lbl.gov:eucx7z_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:eucx7z_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:wxyw0l_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:wxyw0l_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:sjpqjv_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:sjpqjv_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 39597c85c..cb8368c70 master -> origin/master b16749e88..f87fd76c6 dials-next -> origin/dials-next Updating 39597c85c..cb8368c70 Fast-forward .../indexing/basis_vector_search/combinations.py | 71 +------ .../basis_vector_search/test_combinations.py | 42 ++++- algorithms/indexing/bravais_settings.py | 40 ++-- algorithms/indexing/indexer.py | 25 +-- algorithms/indexing/lattice_search/__init__.py | 7 +- algorithms/indexing/stills_indexer.py | 21 +-- algorithms/indexing/symmetry.py | 208 +++++++++------------ algorithms/indexing/test_symmetry.py | 54 +++++- algorithms/scaling/scaling_library.py | 3 +- algorithms/scaling/test_scaling_library.py | 15 +- algorithms/symmetry/__init__.py | 5 + .../symmetry/cosym/test_cosym_analyse_datasets.py | 1 + algorithms/symmetry/laue_group.py | 9 +- algorithms/symmetry/test_laue_group.py | 61 ++++-- command_line/plugins.py | 4 + command_line/refine_bravais_settings.py | 2 +- command_line/symmetry.py | 11 +- command_line/two_theta_refine.py | 18 +- newsfragments/1214.feature | 5 + newsfragments/1217.bugfix | 1 + newsfragments/1226.feature | 4 + test/command_line/test_export.py | 34 ++++ test/command_line/test_refine_bravais_settings.py | 55 +++++- test/command_line/test_two_theta_refine.py | 43 +++-- util/export_mtz.py | 9 +- 25 files changed, 440 insertions(+), 308 deletions(-) create mode 100644 newsfragments/1214.feature create mode 100644 newsfragments/1217.bugfix create mode 100644 newsfragments/1226.feature Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 6b5d5e3..606c095 multiwavelength_nexus -> origin/multiwavelength_nexus * [new branch] nexus_spectra2 -> origin/nexus_spectra2 + 1564647...dd955f5 spectrum_beam2 -> origin/spectrum_beam2 (forced update) Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. svn: E155004: Run 'svn cleanup' to remove locks (type 'svn help cleanup' for details) svn: E155004: Working copy 'C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\ccp4io_adaptbx' locked. svn: E155004: 'C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\ccp4io_adaptbx' is already locked. ===== 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 Process failed with return code 1