13/09/2019 12:00:23.79 13/09/2019 12:00:24.21 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\ & ) C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty conda_base /MIR /COPYALL 1>nul ) & rmdir /S /Q conda_base\ & ) 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 ed32b2778..59f8a2197 master -> origin/master Updating ed32b2778..59f8a2197 Fast-forward cctbx/geometry_restraints/energies.py | 13 +++- crys3d/hklview/NGL_HKLviewerGui.py | 21 +++++- crys3d/hklview/cmdlineframes.py | 35 ++++++--- crys3d/hklview/jsview_3d.py | 85 +++++++++++++++++----- .../secondary_structure/tst_annotation.py | 3 +- libtbx/sphinx/phil.py | 18 ++--- libtbx/sphinx/pubmed.py | 22 +++--- libtbx/sphinx/python_string.py | 10 +-- mmtbx/model/statistics.py | 4 +- mmtbx/monomer_library/pdb_interpretation.py | 7 +- mmtbx/monomer_library/tst_pdb_interpretation.py | 2 +- mmtbx/regression/tst_utils.py | 2 +- mmtbx/secondary_structure/find_ss_from_ca.py | 1 + 13 files changed, 154 insertions(+), 69 deletions(-) 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 7d2470b..d9d1f1e master -> origin/master * [new branch] FormatNexusEigerDLS16M -> origin/FormatNexusEigerDLS16M Updating 7d2470b..d9d1f1e Fast-forward __init__.py | 4 +- command_line/debug_memory.py | 2 +- command_line/depends_on.py | 5 +- command_line/detector_superpose.py | 20 ++++---- command_line/display_parallax_correction.py | 11 ++-- command_line/dlsnxs2cbf.py | 9 ++-- command_line/export_bitmaps.py | 28 +++++----- command_line/image2pickle.py | 16 +++--- command_line/image_average.py | 9 ++-- command_line/import_datablock.py | 5 +- command_line/install_format.py | 6 +-- command_line/overload.py | 8 +-- command_line/plot_detector_models.py | 21 ++++---- command_line/print_beam_centre.py | 7 ++- command_line/print_header.py | 12 +++-- command_line/print_matching_images.py | 9 ++-- command_line/print_sweep.py | 8 +-- command_line/print_sweep_check.py | 8 +-- command_line/radial_average.py | 15 +++--- command_line/read_sweep.py | 7 ++- command_line/saturation.py | 8 +-- command_line/serialize.py | 9 ++-- command_line/to_ewald_sphere.py | 9 ++-- command_line/to_xds.py | 7 +-- .../PILATUS_2M_S_N_24_0107_Diamond.py | 5 +- .../PILATUS_300K_S_N_3_0104_Diamond.py | 5 +- data/beamline_defs/__init__.py | 10 ++-- datablock.py | 19 ++++--- example/resolution_corners.py | 14 ++--- example/to_xds.py | 7 +-- ext.py | 2 +- filecache.py | 3 +- filecache_controller.py | 3 +- format/Format.py | 33 ++++++------ format/FormatBruker.py | 10 ++-- format/FormatBrukerFixedChi.py | 13 ++--- format/FormatBrukerPhotonII.py | 7 +-- format/FormatCBF.py | 8 +-- format/FormatCBFCspad.py | 15 +++--- format/FormatCBFFull.py | 14 +++-- format/FormatCBFFullPilatus.py | 18 +++---- format/FormatCBFFullPilatusDLS300KSN104.py | 8 ++- format/FormatCBFFullPilatusDLS6MSN100.py | 4 +- format/FormatCBFFullPilatusDLS6MSN126.py | 9 ++-- format/FormatCBFMini.py | 25 ++++----- format/FormatCBFMiniADSCHF4M.py | 24 ++++----- format/FormatCBFMiniEiger.py | 19 +++---- format/FormatCBFMiniEigerDLS16MSN160.py | 9 ++-- format/FormatCBFMiniEigerMaxIVBio.py | 5 +- format/FormatCBFMiniEigerPetraP14.py | 5 +- format/FormatCBFMiniEigerPhotonFactory.py | 11 ++-- format/FormatCBFMiniPilatus.py | 7 +-- format/FormatCBFMiniPilatus3APS19ID6MSN132.py | 5 +- format/FormatCBFMiniPilatusDESY6MSN115.py | 5 +- format/FormatCBFMiniPilatusDLS12M.py | 28 ++++------ format/FormatCBFMiniPilatusDLS6MSN100.py | 30 ++++------- format/FormatCBFMiniPilatusDLS6MSN114.py | 5 +- format/FormatCBFMiniPilatusDLS6MSN114DMM.py | 8 ++- format/FormatCBFMiniPilatusDLS6MSN119.py | 5 +- format/FormatCBFMiniPilatusDLS6MSN126.py | 24 +++------ format/FormatCBFMiniPilatusSOLEILPX16MSN106.py | 9 ++-- format/FormatCBFMultiTile.py | 15 +++--- format/FormatCBFMultiTileHierarchy.py | 13 +++-- format/FormatDIP2030b.py | 11 ++-- format/FormatEDFALS733.py | 10 ++-- format/FormatEiger0MQDump.py | 15 +++--- format/FormatEigerStream.py | 53 +++++++++---------- format/FormatGatanDM4.py | 33 +++++------- format/FormatHDF5.py | 6 +-- format/FormatHDF5Dectris.py | 9 ++-- format/FormatHDF5EigerNearlyNexus.py | 40 +++++++-------- format/FormatHDF5EigerNearlyNexusSPring8.py | 8 +-- format/FormatHDF5Lambda.py | 22 ++++---- format/FormatHDF5PAL.py | 16 +++--- format/FormatHDF5RawData.py | 14 +++-- format/FormatHDF5Sacla.py | 20 ++++---- format/FormatHDF5SaclaMPCCD.py | 21 ++++---- format/FormatHDF5SaclaRayonix.py | 20 +++----- format/FormatMarIP.py | 9 ++-- format/FormatMultiImage.py | 12 ++--- format/FormatMultiImageLazy.py | 1 + format/FormatNexus.py | 41 ++++++++++----- format/FormatNexusEigerDLS16M.py | 17 +++---- format/FormatNexusExternalDataFile.py | 8 +-- format/FormatPY.py | 6 +-- format/FormatPYmultitile.py | 12 +++-- format/FormatPYunspecified.py | 18 ++++--- format/FormatPYunspecifiedStill.py | 14 ++--- format/FormatPilatusHelpers.py | 3 +- format/FormatRAXIS.py | 12 ++--- format/FormatRAXISII.py | 9 ++-- format/FormatSER.py | 13 +++-- format/FormatSEReBIC.py | 4 +- format/FormatSMV.py | 7 +-- format/FormatSMVADSC.py | 11 ++-- format/FormatSMVADSCDBG.py | 9 ++-- format/FormatSMVADSCNoDateStamp.py | 8 ++- format/FormatSMVADSCSN.py | 9 ++-- format/FormatSMVADSCSN928.py | 4 +- format/FormatSMVADSCSNAPSID19.py | 5 +- format/FormatSMVADSCmlfsom.py | 5 +- format/FormatSMVCMOS1.py | 17 +++---- format/FormatSMVHamamatsu.py | 4 +- format/FormatSMVHamamatsuSPring8BL32XU.py | 4 +- format/FormatSMVJHSim.py | 11 ++-- format/FormatSMVNOIR.py | 12 ++--- format/FormatSMVRigaku.py | 4 +- format/FormatSMVRigakuA200.py | 11 ++-- format/FormatSMVRigakuA200SPring8BL26B1.py | 4 +- format/FormatSMVRigakuEiger.py | 18 +++---- format/FormatSMVRigakuPilatus.py | 16 +++--- format/FormatSMVRigakuSaturn.py | 12 ++--- format/FormatSMVRigakuSaturnNoTS.py | 10 ++-- format/FormatSMVRigakuSaturnSN07400090.py | 8 +-- format/FormatSMVRigakuSaturnSN09040159.py | 8 +-- format/FormatSMVRigakuSaturnSN11480296.py | 8 +-- format/FormatSMVTimePix_SU.py | 14 ++--- format/FormatStill.py | 3 +- format/FormatTIFF.py | 10 ++-- format/FormatTIFFBruker.py | 15 +++--- format/FormatTIFFHelpers.py | 5 +- format/FormatTIFFRayonix.py | 15 +++--- format/FormatTIFFRayonixESRF.py | 10 ++-- format/FormatTIFFRayonixSPring8.py | 4 +- format/FormatTIFFRayonixXPP.py | 10 ++-- format/FormatXDS.py | 19 +++---- format/FormatXTC.py | 17 +++---- format/FormatXTCCspad.py | 27 +++++----- format/FormatXTCJungfrau.py | 23 ++++----- format/FormatXTCMultipleDetectors.py | 12 ++--- format/FormatXTCRayonix.py | 13 +++-- format/Registry.py | 3 +- format/TemplatePYCXI31.py | 5 +- format/TemplatePYCXI32.py | 5 +- format/TemplatePYCXI41.py | 5 +- format/TemplatePYCXI51.py | 5 +- format/TemplatePYCXI61.py | 5 +- format/TemplatePYCXI71.py | 5 +- format/TemplatePYCXI7d.py | 5 +- format/cbf_writer.py | 33 +++++------- format/nexus.py | 59 ++++++++-------------- format/test_cbf_mini_as_file.py | 16 ++++-- imageset.py | 23 +++++---- libtbx_refresh.py | 14 ++--- masking/__init__.py | 16 +++--- masking/test_masking.py | 14 +++-- model/__init__.py | 32 ++++++------ model/beam.py | 7 ++- model/crystal.py | 12 ++--- model/detector.py | 45 +++++++++-------- model/detector_helpers.py | 2 +- model/detector_helpers_types.py | 4 +- model/experiment_list.py | 9 ++-- model/goniometer.py | 7 ++- model/profile.py | 1 + model/scan.py | 10 ++-- model/scan_helpers.py | 7 ++- newsfragments/85.bugfix | 1 + pyproject.toml | 10 ++++ serialize/dump.py | 7 ++- serialize/filename.py | 2 +- serialize/imageset.py | 5 +- serialize/load.py | 12 ++--- serialize/xds.py | 40 ++++++--------- sweep_filenames.py | 3 +- tests/command_line/test_to_xds.py | 3 +- .../format/test_FormatCBFFullPilatusDLS6MSN126.py | 5 +- tests/format/test_FormatCBFMiniEigerDLS16MSN160.py | 2 +- tests/format/test_FormatHDF5EigerNearlyNexus.py | 1 + .../test_FormatHDF5EigerNearlyNexusSPring8.py | 1 + tests/format/test_FormatHDF5SaclaMPCCD.py | 5 +- tests/format/test_FormatNexus.py | 1 + tests/format/test_FormatNexusEigerDLS16M.py | 41 +++++++++++++-- tests/format/test_FormatPYunspecified.py | 1 + tests/model/crystal_model_old.py | 27 ++++------ tests/model/test_beam.py | 5 +- tests/model/test_crystal_model.py | 22 ++++---- tests/model/test_detector.py | 11 ++-- tests/model/test_detector2.py | 23 +++++---- tests/model/test_experiment_list.py | 3 +- tests/model/test_parallax_correction.py | 8 +-- tests/model/test_pickle.py | 4 +- tests/model/test_pixel_to_millimeter.py | 21 ++++---- tests/model/test_profile.py | 3 +- tests/model/test_ray_intersection.py | 11 ++-- tests/model/test_scan.py | 4 +- tests/model/test_scan_data.py | 11 ++-- tests/model/test_scan_helpers.py | 10 ++-- tests/model/test_to_from_dict.py | 13 ++--- tests/serialize/test_crystal_model_serialize.py | 6 +-- tests/serialize/test_filename.py | 3 +- tests/serialize/test_serialize.py | 30 +++++------ tests/serialize/test_xds.py | 3 +- tests/test_FormatCBFFull.py | 16 ++---- tests/test_beamline_definitions.py | 6 +-- tests/test_crystal_model_equivalence.py | 12 +++-- tests/test_datablock.py | 7 +-- tests/test_detector.py | 4 +- tests/test_filecache.py | 6 +-- tests/test_filecache_controller.py | 5 +- tests/test_goniometer.py | 29 +++++------ tests/test_image_readers.py | 46 ++++++++--------- tests/test_imageset.py | 22 +++----- tests/test_python3_violations.py | 7 +-- tests/test_regression_images.py | 28 +++++----- tests/test_scan.py | 8 +-- tests/test_split_singleimage_datablock.py | 6 ++- 207 files changed, 1163 insertions(+), 1327 deletions(-) create mode 100644 newsfragments/85.bugfix 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 362 files Bootstrap success: cleanup, hot, update 13/09/2019 12:01:58.56 13/09/2019 12:01:58.63 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\ & ) 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. Using default conda installation Base conda installation: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\mc3 Installing cctbx environment with: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\conda_envs\cctbx_py27_win-64.txt Completed installation into: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base Python: 2.7.15 "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\python.exe" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False Python3 migration warning policy: None command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build Top-down list of all modules involved: wxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\wxtbx" gltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx" mmtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx" dxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\ucif" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" cctbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\fable" omptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\boost" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\fable\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_projecDEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. t\iotbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\wxtbx\command_line" requirement dials-data>=2.0.30 is not currently met, package not installed attempting install of dials-data>=2.0.30... Collecting dials-data>=2.0.30 Using cached https://files.pythonhosted.org/packages/e3/7e/a58b6a6d3b7cbd734ab7540d5bf2af6777dbac0a87633ec002239ee4d1e1/dials_data-2.0.40-py2.py3-none-any.whl Requirement already satisfied: pytest in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (3.10.1) Collecting pyyaml (from dials-data>=2.0.30) Using cached https://files.pythonhosted.org/packages/da/7e/b82dad5d7343eb3d53cf84aaefb53515a659c55b1cb7c328287256c1c156/PyYAML-5.1.2-cp27-cp27m-win_amd64.whl Requirement already satisfied: setuptools in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (40.8.0) Requirement already satisfied: six in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (1.12.0) Requirement already satisfied: py>=1.5.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.7.0) Requirement already satisfied: attrs>=17.4.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (18.2.0) Requirement already satisfied: more-itertools>=4.0.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (4.3.0) Requirement already satisfied: atomicwrites>=1.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.3.0) Requirement already satisfied: pluggy>=0.7 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (0.8.1) Requirement already satisfied: pathlib2>=2.2.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (2.3.3) Requirement already satisfied: funcsigs in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.0.2) Requirement already satisfied: colorama in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (0.4.1) Requirement already satisfied: scandir; python_version < "3.5" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pathlib2>=2.2.0->pytest->dials-data>=2.0.30) (1.9.0) Installing collected packages: pyyaml, dials-data The script dials.data.exe is installed in 'C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed dials-data-2.0.40 pyyaml-5.1.2 install successful requires mock>=2.0, has 2.0.0 requirement procrunner>=1.0.2 is not currently met, current version 0.9.0 attempting update of procrunner>=1.0.2... Collecting procrunner>=1.0.2 Using cached https://files.pythonhosted.org/packages/66/16/de3bb5b86261d41e7910c38409d90dd36c15e8398e791c6cffb78fcd9801/procrunner-1.0.2-py2.py3-none-any.whl Requirement already satisfied: six in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from procrunner>=1.0.2) (1.12.0) Requirement already satisfied: pywin32; sys_platform == "win32" and python_version == "2.7" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from procrunner>=1.0.2) (221) Installing collected packages: procrunner Found existing installation: procrunner 0.9.0 Uninstalling procrunner-0.9.0: Successfully uninstalled procrunner-0.9.0 Successfully installed procrunner-1.0.2 update successful requirement pytest<5.0,>=4.5 is not currently met, current version 3.10.1 attempting update of pytest<5.0,>=4.5... Collecting pytest<5.0,>=4.5 Using cached https://files.pythonhosted.org/packages/97/72/d4d6d22ad216f149685f2e93ce9280df9f36cbbc87fa546641ac92f22766/pytest-4.6.5-py2.py3-none-any.whl Requirement already satisfied: funcsigs>=1.0; python_version < "3.0" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (1.0.2) Requirement already satisfied: packaging in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (19.0) Collecting importlib-metadata>=0.12 (from pytest<5.0,>=4.5) Using cached https://files.pythonhosted.org/packages/ba/15/29e4fe1624373be313b5a2565d72ca9121a37f40472112f46eda8dc1235b/importlib_metadata-0.22-py2.py3-none-any.whl Requirement already satisfied: six>=1.10.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (1.12.0) Collecting pluggy<1.0,>=0.12 (from pytest<5.0,>=4.5) Using cached https://files.pythonhosted.org/packages/92/c7/48439f7d5fd6bddb4c04b850bb862b42e3e2b98570040dfaf68aedd8114b/pluggy-0.13.0-py2.py3-none-any.whl Requirement already satisfied: attrs>=17.4.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (18.2.0) Requirement already satisfied: pathlib2>=2.2.0; python_version < "3.6" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (2.3.3) Requirement already satisfied: py>=1.5.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (1.7.0) Requirement already satisfied: atomicwrites>=1.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (1.3.0) Requirement already satisfied: wcwidth in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (0.1.7) Requirement already satisfied: colorama; sys_platform == "win32" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (0.4.1) Requirement already satisfied: more-itertools<6.0.0,>=4.0.0; python_version <= "2.7" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest<5.0,>=4.5) (4.3.0) Requirement already satisfied: pyparsing>=2.0.2 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from packaging->pytest<5.0,>=4.5) (2.3.1) Collecting zipp>=0.5 (from importlib-metadata>=0.12->pytest<5.0,>=4.5) Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl Collecting contextlib2; python_version < "3" (from importlib-metadata>=0.12->pytest<5.0,>=4.5) Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl Collecting configparser>=3.5; python_version < "3" (from importlib-metadata>=0.12->pytest<5.0,>=4.5) Using cached https://files.pythonhosted.org/packages/7a/2a/95ed0501cf5d8709490b1d3a3f9b5cf340da6c433f896bbe9ce08dbe6785/configparser-4.0.2-py2.py3-none-any.whl Requirement already satisfied: scandir; python_version < "3.5" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pathlib2>=2.2.0; python_version < "3.6"->pytest<5.0,>=4.5) (1.9.0) Installing collected packages: zipp, contextlib2, configparser, importlib-metadata, pluggy, pytest Found existing installation: pluggy 0.8.1 Uninstalling pluggy-0.8.1: Successfully uninstalled pluggy-0.8.1 Found existing installation: pytest 3.10.1 Uninstalling pytest-3.10.1: Successfully uninstalled pytest-3.10.1 The scripts py.test.exe and pytest.exe are installed in 'C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed configparser-4.0.2 contextlib2-0.5.5 importlib-metadata-0.22 pluggy-0.13.0 pytest-4.6.5 zipp-0.6.0 update successful Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx\libtbx_refresh.py" Generating C++ header files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\scitbx\array_family" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\scitbx\array_family\boost_python" Using fable to convert scitbx\lbfgs.f Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\cctbx\eltbx" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\cctbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\libtbx_refresh.py" Copying to lib: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib\pycbf\pycbf.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\smtbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx\libtbx_refresh.py" Using fable to convert iotbx\pdb\hybrid_36_f.f Writing: iotbx\pdb\hybrid_36_fem.cpp Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx\libtbx_refresh.py" Enumerating format classes: found FormatBruker based on ['Format'] found FormatBrukerFixedChi based on ['FormatBruker'] found FormatBrukerPhotonII based on ['FormatBruker'] found FormatCBF based on ['Format'] found FormatCBFCspad based on ['FormatCBFMultiTileHierarchyStill'] found FormatCBFFullStillInMemory based on ['FormatCBFFullStill'] found FormatCBFMultiTileHierarchyStillInMemory based on ['FormatCBFFullStillInMemory', 'FormatCBFMultiTileHierarchyStill'] found FormatCBFCspadInMemory based on ['FormatCBFMultiTileHierarchyStillInMemory', 'FormatCBFCspad'] found FormatCBFFull based on ['FormatCBF'] found FormatCBFFullStill based on ['FormatStill', 'FormatCBFFull'] found FormatCBFFullPilatus based on ['FormatCBFFull'] found FormatCBFFullPilatusDLS300KSN104 based on ['FormatCBFFullPilatus'] found FormatCBFFullPilatusDLS6MSN100 based on ['FormatCBFFullPilatus'] found FormatCBFFullPilatusDLS6MSN126 based on ['FormatCBFFullPilatus'] found FormatCBFMini based on ['FormatCBF'] found FormatCBFMiniADSCHF4M based on ['FormatCBFMini'] found FormatCBFMiniEiger based on ['FormatCBFMini'] found FormatCBFMiniEigerDLS16MSN160 based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerMaxIVBio based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerPetraP14 based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerPhotonFactory based on ['FormatCBFMini'] found FormatCBFMiniPilatus based on ['FormatCBFMini'] found FormatCBFMiniPilatus3AOS19ID6MSN132 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusCHESS_6MSN127 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDESY6MSN115 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS12M based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN100 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN114 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN114DMM based on ['FormatCBFMiniPilatus', 'FormatStill'] found FormatCBFMiniPilatusDLS6MSN119 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN126 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusSOLEILPX16MSN106 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusSPring8_6MSN125 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusXXX based on ['FormatCBFMiniPilatus'] found FormatCBFMultiTile based on ['FormatCBFFull'] found FormatCBFMultiTileStill based on ['FormatStill', 'FormatCBFMultiTile'] found FormatCBFMultiTileHierarchy based on ['FormatCBFMultiTile'] found FormatCBFMultiTileHierarchyStill based on ['FormatCBFMultiTileStill', 'FormatCBFMultiTileHierarchy'] found FormatDIP2030b based on ['Format'] found FormatEDFALS733 based on ['Format'] found FormatEiger0MQDump based on ['Format'] found FormatEigerStream based on ['FormatMultiImage', 'Format'] found FormatGatanDM4 based on ['FormatMultiImage', 'Format'] found FormatHDF5 based on ['FormatMultiImage', 'Format'] found FormatHDF5Dectris based on ['FormatHDF5'] found FormatHDF5EigerNearlyNexus based on ['FormatHDF5'] found FormatHDF5EigerNearlyNexusSPring8 based on ['FormatHDF5EigerNearlyNexus'] found FormatHDF5Lambda based on ['FormatHDF5'] found FormatHDF5PAL based on ['FormatHDF5'] found FormatRawData based on ['FormatHDF5'] found FormatHDF5Sacla based on ['FormatHDF5', 'FormatStill'] found FormatHDF5SaclaMPCCD based on ['FormatHDF5', 'FormatStill'] found FormatHDF5SaclaRayonix based on ['FormatHDF5', 'FormatStill'] found FormatMarIP based on ['Format'] found FormatMultiImage based on ['Format'] found FormatMultiImageLazy based on ['FormatMultiImage'] found FormatNexus based on ['FormatHDF5'] found FormatNexusStill based on ['FormatMultiImageLazy', 'FormatNexus', 'FormatStill'] found FormatNexusEigerDLS16M based on ['FormatNexus'] found FormatNexusExternalDataFile based on ['FormatHDF5'] found FormatPY based on ['Format'] found FormatPYmultitile based on ['FormatPY'] found FormatPYunspecified based on ['FormatPY'] found FormatPYunspecifiedInMemory based on ['FormatPYunspecified'] found FormatPYunspecifiedStill based on ['FormatStill', 'FormatPYunspecified'] found FormatPYunspecifiedStillInMemory based on ['FormatStill', 'FormatPYunspecifiedInMemory'] found FormatRAXIS based on ['Format'] found FormatRAXISII based on ['Format'] found FormatRAXISIVSPring8 based on ['Format'] found FormatSER based on ['FormatMultiImage', 'Format'] found FormatSEReBIC based on ['FormatSER'] found FormatSMV based on ['Format'] found FormatSMVADSC based on ['FormatSMV'] found FormatSMVADSCDBG based on ['FormatSMVADSC'] found FormatSMVADSCNoDateStamp based on ['FormatSMVADSC'] found FormatSMVADSCSN based on ['FormatSMVADSC'] found FormatSMVADSCSN445 based on ['FormatSMVADSCSN'] found FormatSMVADSCSNSN457 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN905 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN915 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN920 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN926 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN928 based on ['FormatSMVADSCSN'] found FormatSMVADSCSNAPSID19 based on ['FormatSMVADSCSN'] found FormatSMVADSCmlfsom based on ['FormatSMVADSC'] found FormatSMVCMOS1 based on ['FormatSMV'] found FormatSMVHamamatsu based on ['FormatSMVADSC'] found FormatSMVHamamatsuSPring8BL32XU based on ['FormatSMVHamamatsu'] found FormatSMVJHSim based on ['FormatSMV'] found FormatSMVNOIR based on ['FormatSMVRigaku'] found FormatSMVRigaku based on ['FormatSMV'] found FormatSMVRigakuA200 based on ['FormatSMVRigaku'] found FormatSMVRigakuA200SPring8BL26B1 based on ['FormatSMVRigakuA200'] found FormatSMVRigakuEiger based on ['FormatSMVRigaku'] found FormatSMVRigakuPilatus based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturn based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturnNoTS based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturnSN07400090 based on ['FormatSMVRigakuSaturn'] found FormatSMVRigakuSaturn09040159 based on ['FormatSMVRigakuSaturnNoTS'] found FormatSMVRigakuSaturnSN11480296 based on ['FormatSMVRigakuSaturn'] found FormatSMVTimePix_SU based on ['FormatSMV'] found FormatSMVTimePix_SU_512x512 based on ['FormatSMVTimePix_SU'] found FormatSMVTimePix_SU_516x516 based on ['FormatSMVTimePix_SU'] found FormatStill based on ['Format'] found FormatTIFF based on ['Format'] found FormatTIFFBruker based on ['FormatTIFF'] found FormatTIFFRayonix based on ['FormatTIFF'] found FormatTIFFRayonixESRF based on ['FormatTIFFRayonix'] found FormatTIFFRayonixSPring8 based on ['FormatTIFFRayonix'] found FormatTIFFRayonixXPP based on ['FormatTIFFRayonix'] found FormatXDS based on ['Format'] found FormatXTC based on ['FormatMultiImageLazy', 'FormatStill', 'Format'] found FormatXTCCspad based on ['FormatXTC'] found FormatXTCJungfrau based on ['FormatXTC'] found FormatXTCJungfrauMonolithic based on ['FormatXTCJungfrau'] found FormatXTCMultipleDetectors based on ['FormatXTCRayonix', 'FormatXTCCspad', 'FormatXTCJungfrau'] found FormatXTCRayonix based on ['FormatXTC'] Updating entry points for dxtbx 117 entries for entry point dxtbx.format Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\gltbx" fonts: 8x13 9x15 10x20 Done. usr+sys time: 0.75 seconds wall clock time: 0.75 seconds usage: scons [OPTION] [TARGET] ... SCons Error: option -j: invalid integer value: 'getbootstrap' Performing actions: base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=cctbx ===== Running in .: deleting dist, tests, tmp removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 2 files ===== Running in .: base ===== Running in build: run configure.py ===== Running in build: save configure command ===== Running in build: libtbx.scons.bat Process failed with return code 2 13/09/2019 12:04:02.41