12/06/2019 6:00:01.61 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 8 90300 8 7437 0 0 7437 0 0:00:12 --:--:-- 0:00:12 10343 100 90300 100 90300 0 0 90300 0 0:00:01 --:--:-- 0:00:01 120k 12/06/2019 6:00:02.67 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:i5r9hf_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:i5r9hf_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:gd3uz0_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:gd3uz0_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:5h0z1e_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:5h0z1e_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:ekk2cy_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:ekk2cy_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 2b430ef41..6cb2ce750 master -> origin/master Updating 2b430ef41..6cb2ce750 Fast-forward .gitignore | 3 + .travis.yml | 2 +- algorithms/indexing/symmetry.py | 2 +- algorithms/scaling/reflection_selection.py | 4 +- algorithms/symmetry/cosym/__init__.py | 31 +++++++- .../symmetry/cosym/test_cosym_analyse_datasets.py | 28 +++++-- command_line/cosym.py | 9 +-- command_line/diffraction_geometry_viewer.py | 92 ---------------------- command_line/generate_tutorial_text.py | 4 +- conftest.py | 9 +++ 10 files changed, 68 insertions(+), 116 deletions(-) delete mode 100644 command_line/diffraction_geometry_viewer.py Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx ab2a81a..f3daa9c master -> origin/master + 5538404...a98c09d py3_testbed2 -> origin/py3_testbed2 (forced update) Updating ab2a81a..f3daa9c Fast-forward .gitignore | 3 +++ .python3-test-failures | 12 ++++++--- conftest.py | 9 +++++++ tests/python3_test_filter.py | 63 ++++++++++++++++++++++---------------------- 4 files changed, 52 insertions(+), 35 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': At revision 4633. Updating 'opt_resources': At revision 6. Updating 'phenix': U phenix\wxGUI2\program_template\get_pdb_validation_report.py U phenix\wxGUI2\program_template\prepare_pdb_deposition.py Updated to revision 12953. 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 4496be27..1fba7f65 master -> origin/master Updating 4496be27..1fba7f65 Fast-forward .gitignore | 4 ++++ conftest.py | 9 +++++++++ 2 files changed, 13 insertions(+) Current branch master is up to date. Updating 'chem_data': Fetching external item into 'chem_data\geostd': External at 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\pdb4amber\pdb4amber.py U amber_adaptbx\tests\files\3cfb\non-les\4phenix_3cfb.pdb A amber_adaptbx\tests\files\3cfb\non-les\4amber_3cfb.rst7 U amber_adaptbx\tests\files\3cfb\non-les\4amber_3cfb.prmtop U amber_adaptbx\tests\files\3cfb\non-les\GOL.mol2 U amber_adaptbx\tests\files\3cfb\non-les\non-les.log U amber_adaptbx\tests\files\3cfb\non-les\SPB.mol2 U amber_adaptbx\tests\files\3cfb\test_AmberPrep Updated to revision 380. Updating 'labelit': At revision 2072. Updating 'elbow': U elbow\elbow\command_line\where_is_that_cif_file.py U elbow\elbow\formats\refine_geo_parser.py Updated to revision 3776. 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