01/06/2019 12:00:24.38 
01/06/2019 12:00:25.12 

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
   3ac19b5b2..732729b22  NGL_HKLviewer           -> origin/NGL_HKLviewer
   04c8c4fe5..b1eb0a043  master                  -> origin/master
   c3ae5169c..828cf901c  mmCIF-label_asym_id-fix -> origin/mmCIF-label_asym_id-fix
Already up to date.
Current branch py3 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%]
Already up to date.
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 431 files

Bootstrap success: cleanup, hot, update
01/06/2019 12:01:58.85 
01/06/2019 12:01:58.96 

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_project\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"
requires mock>=2.0, has 2.0.0
requires pytest>=3.1, has 3.10.1
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"
********************************************************************************************************************************************
Warning: unexpected md5 hexdigest:
  File: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\reference_table.py"
  New md5 hexdigest: b4d948c292357b90c8b4d5716d607bb9
  Files to review:
    sgtbx/direct_space_asu/reference_table.py
    cctbx/libtbx_refresh.py
********************************************************************************************************************************************
***************************************************************************************************************************************
Warning: unexpected md5 hexdigest:
  File: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\short_cuts.py"
  New md5 hexdigest: 18e5b9d93962d70711497de1d6dbebbb
  Files to review:
    sgtbx/direct_space_asu/short_cuts.py
    cctbx/libtbx_refresh.py
***************************************************************************************************************************************
*********************************************************************************************************************************************************
Warning: unexpected md5 hexdigest:
  File: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\proto\generate_cpp_asu_table.py"
  New md5 hexdigest: 0f19e51b469650aa23e81483051eeb10
  Files to review:
    sgtbx/direct_space_asu/proto/generate_cpp_asu_table.py
    cctbx/libtbx_refresh.py
*********************************************************************************************************************************************************
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"
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: 0.91 seconds
wall clock time: 0.91 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
01/06/2019 12:04:55.17