02/06/2019 6:00:01.32 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 90030 100 90030 0 0 90030 0 0:00:01 --:--:-- 0:00:01 331k 02/06/2019 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:q1iuzl_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:q1iuzl_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:accrq7_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:accrq7_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:ugcxp4_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:ugcxp4_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:0z2ram_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:0z2ram_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 1e96fffaf..4fb77c819 master -> origin/master Updating 1e96fffaf..4fb77c819 Fast-forward pychef/SConscript | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx c7f0162..8e77cf1 master -> origin/master * [new branch] format-registration -> origin/format-registration Updating c7f0162..8e77cf1 Fast-forward filecache_controller.py | 10 +++++++--- libtbx_refresh.py | 50 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+), 3 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': At revision 12940. 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. Already up to date. 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 3772. 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