06/06/2019 6:00:01.60 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 90301 100 90301 0 0 90301 0 0:00:01 --:--:-- 0:00:01 352k 06/06/2019 6:00:02.18 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:xyjh1v_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:xyjh1v_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:yfwnkc_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:yfwnkc_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:5edyqs_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:5edyqs_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:del3g1_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:del3g1_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 4fb77c819..0d9ed724f master -> origin/master * [new branch] cosym_bad_input -> origin/cosym_bad_input * [new branch] dev-1.14 -> origin/dev-1.14 19190e3b9..1c04ca8dd dials-1.14 -> origin/dials-1.14 052723294..cd06fd9ae dials-next -> origin/dials-next + 335f56d2d...9d80920bb index-refactor -> origin/index-refactor (forced update) + 66662f755...1c2f3842e stills_imgview -> origin/stills_imgview (forced update) Updating 4fb77c819..0d9ed724f Fast-forward algorithms/scaling/scaler.py | 16 --- algorithms/scaling/scaling_options.py | 2 +- algorithms/scaling/test_scale.py | 15 --- algorithms/scaling/test_scale_and_filter.py | 1 - algorithms/scaling/test_scaler.py | 13 +- algorithms/spot_finding/per_image_analysis.py | 170 +++++++++++--------------- command_line/reciprocal_lattice_viewer.py | 104 ++++------------ command_line/scale.py | 67 ++++------ installer/dials_installer.py | 8 +- 9 files changed, 134 insertions(+), 262 deletions(-) Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 8e77cf1..b21bf4c master -> origin/master Updating 8e77cf1..b21bf4c Fast-forward format/FormatCBFMiniEiger.py | 51 +----------------------------- format/FormatPilatusHelpers.py | 72 ++++++++++++++++++++++++++---------------- 2 files changed, 45 insertions(+), 78 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': U phenix_regression\mmtbx\geometry_minimization\tst_00.py U phenix_regression\validation\tst_molprobity_consistency.py Updated to revision 4630. Updating 'opt_resources': At revision 6. Updating 'phenix': U phenix\phenix\refinement\nqh_flips.py Updated to revision 12941. 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 0d61d306..1c377b3a master -> origin/master b176367e..5f4e2fb3 dials-1.14 -> origin/dials-1.14 c60801a9..4170f675 dials-next -> origin/dials-next * [new branch] report-refactor -> origin/report-refactor Updating 0d61d306..1c377b3a Fast-forward Handlers/CommandLine.py | 17 +++++++++++++++++ Handlers/test_CommandLine.py | 23 +++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 Handlers/test_CommandLine.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': U phenix_html\rst_files\faqs\cryo_fit_FAQ.txt Updated to revision 1327. 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\__init__.py U amber_adaptbx\utils.py U amber_adaptbx\les_builder\build.py U amber_adaptbx\pdb4amber\pdb4amber.py U amber_adaptbx\pdb4amber\utils.py U amber_adaptbx\amber_manual.txt Updated to revision 365. Updating 'labelit': At revision 2072. Updating 'elbow': U elbow\elbow\utilities\refine_inputs.py Updated to revision 3773. 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