22/10/2019 12:00:24.43 22/10/2019 12:00:24.99 C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\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\CCTBXVC2008\x64\Current>((ROBOCOPY empty build /MIR /COPYALL 1>nul ) & rmdir /S /Q build\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\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 ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from annlib.gz ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from scons.gz ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from ccp4io.gz ===== Downloading http://cci.lbl.gov/repositories/eigen.gz: 1.5 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from eigen.gz ===== Downloading http://cci.lbl.gov/repositories/clipper.gz: 0.6 MB [0%.........20%.........40%.........60%.........80%.........100%] Already up to date. Current branch master is up to date. From https://github.com/cctbx/cctbx_project 84ed18018..911d22155 master -> origin/master 1ce21cf16..391862974 LS49_exp -> origin/LS49_exp 8b6dccc84..c6e7de1d3 diffBragg -> origin/diffBragg + b84bc07cb...34e21260b xfel_datasets -> origin/xfel_datasets (forced update) Updating 84ed18018..911d22155 Fast-forward cctbx/miller/__init__.py | 6 +- iotbx/run_tests.py | 12 +- libtbx/pkg_utils.py | 5 +- mmtbx/command_line/rama_z.py | 19 ++ mmtbx/programs/rama_z.py | 48 +++++ mmtbx/regression/tst_rama_z_01.py | 48 +++++ mmtbx/run_tests.py | 1 + mmtbx/validation/rama_z.py | 231 +++++++++++++++++++++ scitbx/libtbx_refresh.py | 9 + xfel/clustering/cluster_groups.py | 9 +- xfel/clustering/command_line/cluster_42.py | 2 +- .../command_line/cluster_intensity_statistics.py | 2 +- .../command_line/cluster_per_frame_wilson.py | 2 +- xfel/clustering/command_line/cluster_unit_cell.py | 2 +- .../command_line/cluster_visualise_orientations.py | 2 +- xfel/clustering/singleframe.py | 7 +- 16 files changed, 383 insertions(+), 22 deletions(-) create mode 100644 mmtbx/command_line/rama_z.py create mode 100644 mmtbx/programs/rama_z.py create mode 100644 mmtbx/regression/tst_rama_z_01.py create mode 100644 mmtbx/validation/rama_z.py Current branch master is up to date. Already up to date. Current branch master is up to date. ===== Running in modules: extracting files from clipper.gz ===== Running in modules\cbflib: git pull --rebase ===== Running in modules\cctbx_project: git pull --rebase ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB [0%.........20%.........40%.........60%.........80%.........100%] From https://github.com/cctbx/dxtbx 6482ce1..869b2b2 master -> origin/master Updating 6482ce1..869b2b2 Fast-forward imageset.h | 1 - tests/test_imageset.py | 19 +++++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) Current branch master is up to date. ===== Running in modules: extracting files from tntbx.gz ===== Running in modules\dxtbx: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: 203.9 kB [0%.........20%.........40%.........60%.........80%.........100%] Already up to date. Current branch master is up to date. ===== Running in modules: extracting files from ccp4io_adaptbx.gz ===== Running in modules\boost: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/gui_resources.gz: 2.1 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from gui_resources.gz removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 0 files Bootstrap success: cleanup, hot, update 22/10/2019 12:01:24.05 22/10/2019 12:01:24.13 Performing actions: base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=cctbx Traceback (most recent call last): File "bootstrap.py", line 2721, in run() File "bootstrap.py", line 2716, in run use_conda=options.use_conda, File "bootstrap.py", line 1119, in __init__ self.add_configure() File "bootstrap.py", line 1753, in add_configure self.python_base = self._get_conda_python() File "bootstrap.py", line 1513, in _get_conda_python m = self._get_conda_manager() File "bootstrap.py", line 1503, in _get_conda_manager check_file=check_file, log=log) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\install_conda.py", line 329, in __init__ env=self.env)) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\install_conda.py", line 57, in check_output returncode = subprocess.check_call(command_list, stdout=f, *args, **kwargs) File "C:\Python27amd64\lib\subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmd', '/c', 'C:\\Users\\phaserbuilder\\PhaserTng2\\mc3\\Scripts\\conda.exe', 'info', '--json']' returned non-zero exit status 1 22/10/2019 12:01:29.02