23/11/2019 12:00:24.18 23/11/2019 12:00:24.48 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 76721dd5c..c8da883c8 master -> origin/master 7ddce3656..c782656bd diffBragg -> origin/diffBragg + 8d705b9d6...9828ba182 newpy -> origin/newpy (forced update) Updating 76721dd5c..c8da883c8 Fast-forward .azure-pipelines/xfel/azure-pipelines-xfel.yml | 3 +- .azure-pipelines/xfel/conda-linux.yml | 5 - .azure-pipelines/xfel/conda-win.yml | 116 ---------------- .azure-pipelines/xfel/download-conda.yml | 57 ++++++++ cctbx/miller/display2.py | 2 +- cctbx/uctbx/determine_unit_cell/SConscript | 7 +- cctbx/uctbx/determine_unit_cell/ext.cpp | 12 ++ crys3d/hklview/NGL_HKLviewerGui.py | 27 +++- crys3d/hklview/cmdlineframes.py | 2 +- crys3d/hklview/jsview_3d.py | 151 +++++++++++++-------- libtbx/auto_build/installer_utils.py | 3 +- libtbx/env_config.py | 15 +- .../tst_mutli_residue.py | 2 +- mmtbx/conformation_dependent_library/tst_rdl.py | 24 ---- .../tst_rna_dna_fragments.py | 2 +- mmtbx/hydrogens/specialised_hydrogen_atoms.py | 131 ++++++++++++++++-- mmtbx/ligands/ready_set_utils.py | 68 +--------- mmtbx/ligands/tst_ready_set_utils.py | 112 +++++++++++++-- 18 files changed, 436 insertions(+), 303 deletions(-) delete mode 100644 .azure-pipelines/xfel/conda-win.yml create mode 100644 .azure-pipelines/xfel/download-conda.yml 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 a6456ab..3365897 master -> origin/master Updating a6456ab..3365897 Fast-forward command_line/detector_superpose.py | 6 +-- command_line/image_average.py | 12 ++--- datablock.py | 92 +++++++++++++++++++------------------- format/FormatCBFCspad.py | 6 +-- format/FormatCBFMultiTile.py | 4 +- format/FormatNexus.py | 4 +- format/FormatPYmultitile.py | 2 +- format/FormatPYunspecified.py | 4 +- format/FormatPYunspecifiedStill.py | 4 +- format/FormatSMVADSCDBG.py | 2 +- format/FormatTIFFRayonixXPP.py | 4 +- format/FormatXTC.py | 10 ++--- format/FormatXTCCspad.py | 2 +- format/FormatXTCJungfrau.py | 4 +- format/FormatXTCRayonix.py | 2 +- format/cbf_writer.py | 8 ++-- format/nexus.py | 2 +- imageset.py | 14 +++--- model/__init__.py | 30 ++++++------- serialize/dump.py | 4 +- serialize/imageset.py | 4 +- serialize/load.py | 6 +-- tests/model/test_detector2.py | 4 +- 23 files changed, 115 insertions(+), 115 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 23/11/2019 12:01:20.18 23/11/2019 12:01:20.24 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 23/11/2019 12:01:25.10