20/11/2019 12:00:24.14 20/11/2019 12:00:24.44 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 34685978d..e523b3aa8 master -> origin/master * [new branch] azure_xfel_testing -> origin/azure_xfel_testing bff5578cb..28b94b4bb diffBragg -> origin/diffBragg + 0bf400ce1...e7078e86e windows_fix -> origin/windows_fix (forced update) Updating 34685978d..e523b3aa8 Fast-forward crys3d/hklview/NGL_HKLviewerGui.py | 37 +++++--- crys3d/hklview/cmdlineframes.py | 10 +- crys3d/hklview/jsview_3d.py | 43 ++++++--- libtbx/phil/__init__.py | 5 +- mmtbx/conformation_dependent_library/__init__.py | 50 ++++++++-- mmtbx/conformation_dependent_library/cdl_setup.py | 17 ++++ .../multi_residue_cdl_class.py | 14 ++- .../tst_cis_c_n_ca.py | 2 +- mmtbx/hydrogens/specialised_hydrogen_atoms.py | 103 +++++++++++++++++++++ mmtbx/ligands/ready_set_utils.py | 9 +- mmtbx/ligands/tst_ready_set_utils.py | 47 ++++++++++ mmtbx/monomer_library/tst_metal_coordination.py | 1 + mmtbx/run_tests.py | 1 + 13 files changed, 296 insertions(+), 43 deletions(-) create mode 100644 mmtbx/hydrogens/specialised_hydrogen_atoms.py create mode 100644 mmtbx/ligands/tst_ready_set_utils.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 476fb84..bc0b3d3 master -> origin/master dd91ef7..448e9a2 load-before-heat-death -> origin/load-before-heat-death + 45e2813...6bdc18e newpy -> origin/newpy (forced update) Updating 476fb84..bc0b3d3 Fast-forward datablock.py | 19 +++--------------- format/Registry.py | 35 --------------------------------- model/__init__.py | 14 -------------- model/experiment_list.py | 17 ---------------- serialize/xds.py | 50 ++++++++---------------------------------------- 5 files changed, 11 insertions(+), 124 deletions(-) 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 20/11/2019 12:01:16.83 20/11/2019 12:01:16.89 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 2766, in run() File "bootstrap.py", line 2761, in run use_conda=options.use_conda, File "bootstrap.py", line 1132, in __init__ self.add_configure() File "bootstrap.py", line 1768, in add_configure self.python_base = self._get_conda_python() File "bootstrap.py", line 1526, in _get_conda_python m = self._get_conda_manager() File "bootstrap.py", line 1516, 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 330, 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 20/11/2019 12:01:20.13