29/05/2019 6:00:01.10 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 90030 100 90030 0 0 90030 0 0:00:01 --:--:-- 0:00:01 224k 29/05/2019 6:00:01.82 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:2fzfle_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:2fzfle_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:ceopam_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:ceopam_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:cld2ot_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:cld2ot_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:m5mxth_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:m5mxth_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 cd74d692f..09e3c9f4a master -> origin/master * [new branch] FPE -> origin/FPE Updating cd74d692f..09e3c9f4a Fast-forward .gitignore | 4 + SConscript | 1 + precommitbx/installer.py | 6 +- pychef/Chef.h | 668 +++++++++++++++++++++++++++++++++++++++++++++++ pychef/SConscript | 7 + pychef/__init__.py | 570 ++++++++++++++++++++++++++++++++++++++++ pychef/ext.cc | 108 ++++++++ pychef/test_pychef.py | 58 ++++ setup.py | 46 ++++ 9 files changed, 1465 insertions(+), 3 deletions(-) create mode 100644 pychef/Chef.h create mode 100644 pychef/SConscript create mode 100644 pychef/__init__.py create mode 100644 pychef/ext.cc create mode 100644 pychef/test_pychef.py create mode 100644 setup.py Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 043d9a1..2a9714d master -> origin/master Updating 043d9a1..2a9714d Fast-forward datablock.py | 40 ++++++++++++++++++++++------------------ model/experiment_list.py | 10 +++++----- serialize/filename.py | 25 ++++++++++++++++++++++++- serialize/imageset.py | 18 +++++++++--------- tests/serialize/test_filename.py | 8 ++++---- 5 files changed, 64 insertions(+), 37 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 4629. Updating 'opt_resources': At revision 6. Updating 'phenix': A phenix\phenix\ligands\hierarchy_utils.py Updated to revision 12938. 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 5f4e5bc8..07302ef4 master -> origin/master Updating 5f4e5bc8..07302ef4 Fast-forward .gitignore | 4 + Decorators/DecoratorFactory.py | 17 +- Driver/ClusterDriverFactory.py | 37 +- Driver/DriverFactory.py | 48 +- Driver/test_ClusterDriverFactory.py | 14 + Driver/test_DriverFactory.py | 14 + Handlers/Syminfo.py | 23 +- Modules/Analysis/__init__.py | 62 ++- Modules/MultiCrystal/ScaleAndMerge.py | 21 +- Modules/MultiCrystalAnalysis.py | 842 +++++++++++++-------------------- Modules/PyChef/Chef.h | 668 -------------------------- Modules/PyChef/SConscript | 9 - Modules/PyChef/__init__.py | 570 ---------------------- Modules/PyChef/ext.cc | 108 ----- SConscript | 24 - Test/Modules/test_Pychef.py | 60 --- Wrappers/XDS/XDSIdxref.py | 33 +- Wrappers/XIA/MultiCrystalAnalysis.py | 73 --- command_line/chef.py | 2 +- command_line/mca.py | 399 ---------------- command_line/multi_crystal_analysis.py | 386 +-------------- command_line/report.py | 561 +--------------------- setup.py | 46 ++ 23 files changed, 536 insertions(+), 3485 deletions(-) create mode 100644 Driver/test_ClusterDriverFactory.py create mode 100644 Driver/test_DriverFactory.py delete mode 100644 Modules/PyChef/Chef.h delete mode 100644 Modules/PyChef/SConscript delete mode 100644 Modules/PyChef/__init__.py delete mode 100644 Modules/PyChef/ext.cc delete mode 100644 SConscript delete mode 100644 Test/Modules/test_Pychef.py delete mode 100644 Wrappers/XIA/MultiCrystalAnalysis.py delete mode 100644 command_line/mca.py create mode 100644 setup.py 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 1326. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Updating 'amber_adaptbx': At revision 363. Updating 'labelit': At revision 2072. Updating 'elbow': At revision 3771. 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