26/11/2019 12:00:23.91 26/11/2019 12:00:24.30 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 63e98cc63..55aad7257 master -> origin/master + 6c324f221...1a39b3dfe test2 -> origin/test2 (forced update) Updating 63e98cc63..55aad7257 Fast-forward .azure-pipelines/azure-pipelines-nightly.yml | 2 +- crys3d/hklview/NGL_HKLviewerGui.py | 6 +- crys3d/hklview/cmdlineframes.py | 2 +- crys3d/hklview/jsview_3d.py | 48 +++++++++------ iota/__init__.py | 4 +- iota/components/iota_analysis.py | 10 +++ iota/components/iota_base.py | 54 +++++++++++++++- iota/components/iota_init.py | 1 + iota/components/iota_processing.py | 19 ++---- iota/components/iota_threads.py | 9 ++- iota/components/iota_ui_frames.py | 22 +++++-- iota/doc/NOTES.txt | 23 +++---- iotbx/data_manager/model.py | 2 + iotbx/pdb/mmcif.py | 2 +- iotbx/xds/xparm.py | 1 - libtbx/program_template.py | 52 ++++++++++++---- libtbx/tst_program_template.py | 14 +++++ .../loop_closure/starting_conformations.py | 2 +- .../metal_coordination_library.py | 2 +- .../testing_utils.py | 25 ++++++++ mmtbx/conformation_dependent_library/tst_rdl.py | 2 + .../torsion_restraints/reference_model.py | 2 +- mmtbx/model/model.py | 1 + mmtbx/monomer_library/tst_linking.py | 4 +- mmtbx/programs/cablam_idealization.py | 4 +- mmtbx/programs/rama_z.py | 71 ++++++++++++++++------ .../ensemble_refinement/ensemble_utils.py | 5 +- .../fix_cablam/tst_basic_cl_operations.py | 1 + mmtbx/regression/tst_multi_residue_class.py | 2 +- mmtbx/secondary_structure/regularize_from_pdb.py | 2 +- mmtbx/validation/cablam.py | 1 + mmtbx/validation/rama_z.py | 1 + mmtbx/validation/utils.py | 2 +- prime/command_line/frame_extractor_by_scan.py | 2 +- .../merging/application/group/group_reflections.py | 2 +- 35 files changed, 302 insertions(+), 100 deletions(-) create mode 100644 mmtbx/conformation_dependent_library/testing_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 3365897..2a91b57 master -> origin/master Updating 3365897..2a91b57 Fast-forward format/FormatGatanDM4.py | 5 ++++- model/scan.h | 5 +++++ run_tests.py | 24 ++++++++---------------- 3 files changed, 17 insertions(+), 17 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 26/11/2019 12:01:20.12 26/11/2019 12:01:20.20 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 26/11/2019 12:01:24.06