Bootstrap build started on Thu Mar 21 15:01:03 2024 ALLUSERSPROFILE=C:\ProgramData APPDATA=C:\Users\phaserbuilder\AppData\Roaming COMMANDPROMPTTYPE=Native COMMONPROGRAMFILES=C:\Program Files\Common Files COMMONPROGRAMFILES(X86)=C:\Program Files (x86)\Common Files COMMONPROGRAMW6432=C:\Program Files\Common Files COMPUTERNAME=AZIMUTH COMSPEC=C:\WINDOWS\system32\cmd.exe DEFLOGDIR=C:\ProgramData\McAfee\Endpoint Security\Logs DEVENVDIR=C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\ DRIVERDATA=C:\Windows\System32\Drivers\DriverData EXTENSIONSDKDIR=C:\Program Files (x86)\Microsoft SDKs\Windows Kits\10\ExtensionSDKs FRAMEWORK40VERSION=v4.0 FRAMEWORKDIR=C:\WINDOWS\Microsoft.NET\Framework64\ FRAMEWORKDIR64=C:\WINDOWS\Microsoft.NET\Framework64 FRAMEWORKVERSION=v4.0.30319 FRAMEWORKVERSION64=v4.0.30319 GIT_SSH=C:\Windows\System32\OpenSSH\ssh.exe HTMLHELPDIR=C:\Program Files (x86)\HTML Help Workshop INCLUDE=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\include;C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\include;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt LIB=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\lib\amd64;C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\lib\amd64;C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\ucrt\x64;C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\um\x64 LIBPATH=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\lib\amd64;C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\lib\amd64;C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\lib\store\references;C:\Program Files (x86)\Windows Kits\10\UnionMetadata\10.0.19041.0;C:\Program Files (x86)\Windows Kits\10\References\10.0.19041.0;C:\WINDOWS\Microsoft.NET\Framework64\v4.0.30319 LOCALAPPDATA=C:\Users\phaserbuilder\AppData\Local NUMBER_OF_PROCESSORS=24 ONEDRIVE=C:\Users\phaserbuilder\OneDrive OS=Windows_NT PATH=C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\\Extensions\Microsoft\IntelliCode\CLI;C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\amd64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\CommonExtensions\Microsoft\TestWindow;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\CommonExtensions\Microsoft\TeamFoundation\Team Explorer;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\MSBuild\Current\bin\Roslyn;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Team Tools\Performance Tools\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Team Tools\Performance Tools;C:\Program Files (x86)\Microsoft Visual Studio\Shared\Common\VSPerfCollectionTools\vs2019\\x64;C:\Program Files (x86)\Microsoft Visual Studio\Shared\Common\VSPerfCollectionTools\vs2019\;C:\Program Files (x86)\HTML Help Workshop;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\devinit;C:\Program Files (x86)\Windows Kits\10\bin\10.0.19041.0\x64;C:\Program Files (x86)\Windows Kits\10\bin\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\\MSBuild\Current\Bin;C:\WINDOWS\Microsoft.NET\Framework64\v4.0.30319;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Utilities;C:\Program Files\TortoiseSVN\bin;C:\Program Files (x86)\NSIS\Unicode;C:\Program Files\Git\cmd;C:\Program Files\PuTTY\;C:\Program Files\TortoiseGit\bin;C:\Program Files\dotnet\;C:\Users\phaserbuilder\AppData\Local\Microsoft\WindowsApps;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\Llvm\x64\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\CommonExtensions\Microsoft\CMake\Ninja;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\IDE\VC\Linux\bin\ConnectionManagerExe PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC;.PY;.PYW PLATFORM=x64 PROCESSOR_ARCHITECTURE=AMD64 PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 44 Stepping 2, GenuineIntel PROCESSOR_LEVEL=6 PROCESSOR_REVISION=2c02 PROGRAMDATA=C:\ProgramData PROGRAMFILES=C:\Program Files PROGRAMFILES(X86)=C:\Program Files (x86) PROGRAMW6432=C:\Program Files PROMPT=$P$G PSMODULEPATH=%ProgramFiles%\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules PUBLIC=C:\Users\Public SYSTEMDRIVE=C: SYSTEMROOT=C:\WINDOWS TEMP=C:\Users\phaserbuilder\AppData\Local\Temp TMP=C:\Users\phaserbuilder\AppData\Local\Temp UCRTVERSION=10.0.19041.0 UNIVERSALCRTSDKDIR=C:\Program Files (x86)\Windows Kits\10\ USERDOMAIN=AZIMUTH USERNAME=phaserbuilder USERPROFILE=C:\Users\phaserbuilder VCIDEINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ VCINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ VCTOOLSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ VCTOOLSREDISTDIR=C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\Redist\ VISUALSTUDIOVERSION=16.0 VS140COMNTOOLS=C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\Tools\ VS160COMNTOOLS=C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\ VSCMD_ARG_APP_PLAT=Desktop VSCMD_ARG_HOST_ARCH=x64 VSCMD_ARG_TGT_ARCH=x64 VSCMD_ARG_VCVARS_VER=14.0 VSCMD_VER=16.11.29 VSINSTALLDIR=C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\ WINDIR=C:\WINDOWS WINDOWSLIBPATH=C:\Program Files (x86)\Windows Kits\10\UnionMetadata\10.0.19041.0;C:\Program Files (x86)\Windows Kits\10\References\10.0.19041.0 WINDOWSSDKBINPATH=C:\Program Files (x86)\Windows Kits\10\bin\ WINDOWSSDKDIR=C:\Program Files (x86)\Windows Kits\10\ WINDOWSSDKLIBVERSION=10.0.19041.0\ WINDOWSSDKVERBINPATH=C:\Program Files (x86)\Windows Kits\10\bin\10.0.19041.0\ WINDOWSSDKVERSION=10.0.19041.0\ __DEVINIT_PATH=C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\devinit\devinit.exe __DOTNET_ADD_64BIT=1 __DOTNET_PREFERRED_BITNESS=64 __VSCMD_PREINIT_PATH=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Utilities;C:\Program Files\TortoiseSVN\bin;C:\Program Files (x86)\NSIS\Unicode;C:\Program Files\Git\cmd;C:\Program Files\PuTTY\;C:\Program Files\TortoiseGit\bin;C:\Program Files\dotnet\;C:\Users\phaserbuilder\AppData\Local\Microsoft\WindowsApps __VSCMD_SCRIPT_ERR_COUNT=0 Using compiler: Microsoft (R) C/C++ Optimizing Compiler Version 19.00.24247.2 for x64 Copyright (C) Microsoft Corporation. All rights reserved. curl https://gitlab.developers.cam.ac.uk/scm/haematology/readgroup/phaser_regression/-/raw/master/MakeRegressionTestContents.py > MakeRegressionTestContents.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 8384 100 8384 0 0 29222 0 --:--:-- --:--:-- --:--:-- 29521 None curl https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py > bootstrap.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 104k 100 104k 0 0 449k 0 --:--:-- --:--:-- --:--:-- 454k None "C:\Program Files\Python38\python.exe" bootstrap.py --builder=voyager --use_conda --verbose --python=38 --nproc=23 update build C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. Already up to date. Already up to date. Already up to date. Already up to date. Already up to date. Already up to date. Already up to date. Writing files containing version information for cctbx_project =============================================================================== Wrote C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\libtbx\..\..\cctbx_project\cctbx_version.txt Wrote C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\libtbx\..\..\cctbx_project\cctbx_version.h Wrote C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\libtbx\..\..\cctbx_project\setup.py =============================================================================== Already up to date. From https://gitlab.developers.cam.ac.uk/scm/haematology/readgroup/phasertng f3289ec5..d250d346 master -> origin/master * [new tag] svnrev_1906_gitrev_1893 -> svnrev_1906_gitrev_1893 Updating f3289ec5..d250d346 Fast-forward codebase/phasertng/boost_python/Output_bpl.cpp | 1 + 1 file changed, 1 insertion(+) Already up to date. Already up to date. Already up to date. Python: 3.8.8 "C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\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: True Boost threads enabled: True Enable CUDA: False Enable KOKKOS: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: True command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build Top-down list of all modules involved: voyager_regression "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\voyager_regression" phaser_voyager "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_voyager" phasertng "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng" phaser_regression "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_regression" phaser "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser" tntbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\tntbx" mmtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx" reduce "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\reduce" iotbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\iotbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\ucif" crys3d "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d" cctbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\fable" cma_es "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cma_es" omptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost" "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\fable\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\iotbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\reduce\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser\phaser\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng\phasertng\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng\phasertng\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_voyager\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\voyager_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx\libtbx_refresh.py" Generating C++ header files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\scitbx\array_family" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\scitbx\array_family\boost_python" Using fable to convert scitbx\lbfgs.f Updating entry points for scitbx 1 entries for entry point pytest_randomly.random_seeder running egg_info writing libtbx.scitbx.egg-info\PKG-INFO writing dependency_links to libtbx.scitbx.egg-info\dependency_links.txt writing entry points to libtbx.scitbx.egg-info\entry_points.txt writing top-level names to libtbx.scitbx.egg-info\top_level.txt reading manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' writing manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\cctbx\eltbx" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\cctbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\smtbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\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\phasertngvc2015\current\modules\reduce\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\exe" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\exe_dev" Done. Base conda installation: C:\Users\phaserbuilder\NightlyBuilds\PhaserPy3VC2008\Current\mc3 conda_setpaths.bat has been written successfully. conda_unsetpaths.bat has been written successfully. scons: Reading SConscript files ... MSVC_VERSION: 14.0 libtbx.scons: OpenMP is available. BOOST_VERSION: 107400 phaser: Distributed version phaser: Generating C++ and libtbx.phil defaults files phaser: Building shared version Access denied - . File not found - -NAME File not found - -EXEC File not found - RM File not found - -RF File not found - {} File not found - \; Checking for C library phaserncs... (cached) yes Found phaserncs library phasertng: Distributed version phasertng: Building shared version scons: done reading SConscript files. scons: Building targets ... link /nologo /OUT:bin\cctbx_blobs.exe /LIBPATH:lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\libs /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Library\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Library\bin /LIBPATH:lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\lib asymmetric_map.lib iotbx_xplor.lib cctbx_sgtbx_asu.lib cctbx.lib omptbx.lib cctbx\maptbx\blobs_cmd.obj cl /Fophasertng\codebase\phasertng\boost_python\Output_bpl.obj /c C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\phasertng\codebase\phasertng\boost_python\Output_bpl.cpp -DBOOST_BIND_GLOBAL_PLACEHOLDERS -DBOOST_ALLOW_DEPRECATED_HEADERS /DBOOST_PYTHON_MAX_ARITY=22 /GR /EHsc /DHAVE_SNPRINTF /DBOOST_PYTHON_MAX_BASES=48 -DUSE_CONDA /nologo /D_SECURE_SCL=0 /D_CRT_SECURE_NO_DEPRECATE /DNOMINMAX /DWIN32 /DDLL_EXPORTS /D_WIN32_WINNT=_WIN32_WINNT_WIN7 /bigobj /wd4996 /wd4068 /Z7 /Zm800 /MD /DNDEBUG /O2 /fp:fast /DBOOST_ALL_NO_LIB /DHAVE_SNPRINTF /openmp /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project /IC:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\include /IC:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Library\include /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng\codebase /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include /Ic:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\ccp4io\libccp4\ccp4 /IC:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Include Output_bpl.cpp link /nologo /incremental:no /dll /MANIFEST c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\phasertng_autogen\Version.obj /out:lib\phasertng_ext.pyd /implib:lib\phasertng_ext.lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\libs /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Library\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\conda_base\Library\bin /LIBPATH:lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\lib /LIBPATH:lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\lib /LIBPATH:C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules\cctbx_project\lib Advapi32.lib phasertng_main.lib phasertng_autogen.lib phaserncs.lib ccp4io.lib cctbx.lib iotbx_pdb.lib mmtbx_masks.lib cctbx_sgtbx_asu.lib boost_system.lib boost_filesystem.lib boost_thread.lib omptbx.lib scitbx_boost_python.lib boost_thread.lib boost_system.lib boost_chrono.lib boost_python38.lib python38.lib phasertng\codebase\phasertng\boost_python\phasertng_ext.obj phasertng\codebase\phasertng\boost_python\Output_bpl.obj phasertng\codebase\phasertng\boost_python\dag_bpl.obj phasertng\codebase\phasertng\boost_python\enum_bpl.obj Creating library lib\phasertng_ext.lib and object lib\phasertng_ext.exp mt /nologo -manifest lib\phasertng_ext.pyd.manifest -outputresource:lib\phasertng_ext.pyd;2 scons: done building targets. scons: Reading SConscript files ... MSVC_VERSION: 14.0 libtbx.scons: OpenMP is available. BOOST_VERSION: 107400 phaser: Distributed version phaser: Generating C++ and libtbx.phil defaults files phaser: Building shared version Access denied - . File not found - -NAME File not found - -EXEC File not found - RM File not found - -RF File not found - {} File not found - \; Checking for C library phaserncs... (cached) yes Found phaserncs library phasertng: Distributed version phasertng: Building shared version scons: done reading SConscript files. scons: Building targets ... scons: `.' is up to date. scons: done building targets. Rebuilding rotarama library skipped. Needs rotamer library. Rebuilding CaBLAM contours skipped. Needs chem_data/cablam_data directory. Python: 3.8.8 "C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\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: True Boost threads enabled: True Enable CUDA: False Enable KOKKOS: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: True command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build Top-down list of all modules involved: voyager_regression "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\voyager_regression" phaser_voyager "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_voyager" phasertng "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng" phaser_regression "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_regression" phaser "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser" tntbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\tntbx" mmtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx" reduce "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\reduce" iotbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\iotbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\ucif" crys3d "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d" cctbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\fable" cma_es "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cma_es" omptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost" "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\fable\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\iotbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\reduce\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser\phaser\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng\phasertng\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phasertng\phasertng\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\phaser_voyager\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\voyager_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\libtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\boost_adaptbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\scitbx\libtbx_refresh.py" Generating C++ header files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\scitbx\array_family" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\scitbx\array_family\boost_python" Using fable to convert scitbx\lbfgs.f Updating entry points for scitbx 1 entries for entry point pytest_randomly.random_seeder running egg_info writing libtbx.scitbx.egg-info\PKG-INFO writing dependency_links to libtbx.scitbx.egg-info\dependency_links.txt writing entry points to libtbx.scitbx.egg-info\entry_points.txt writing top-level names to libtbx.scitbx.egg-info\top_level.txt reading manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' writing manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\cctbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\cctbx\eltbx" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\cctbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\crys3d\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\smtbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\include\smtbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\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\phasertngvc2015\current\modules\reduce\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\modules\cctbx_project\mmtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\exe" Processing: "c:\users\phaserbuilder\nightlybuilds\phasertngvc2015\current\build\exe_dev" Done. Performing actions: update build ===== Running in .: deleting dist, tests, tmp ===== Running in modules\tntbx: git pull --rebase ===== Running in modules\phaser: git pull --rebase ===== Running in modules\annlib: git pull --rebase ===== Running in modules\phaser_voyager: git pull --rebase ===== Running in modules\ccp4io: git pull --rebase WARNING: Can not update existing git repository! You are not on a branch. This may be legitimate when run eg. via Jenkins, but be aware that you cannot commit any changes ===== Running in modules\reduce: git pull --rebase ===== Running in modules\cctbx_project: git pull --rebase ===== Running in modules\cctbx_project: C:\Program Files\Python38\python.exe libtbx\version.py ===== Running in modules\phaser_regression: git pull --rebase ===== Running in modules\phasertng: git pull --rebase ===== Running in modules\ccp4io_adaptbx: git pull --rebase ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Running in modules\voyager_regression: git pull --rebase removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules, walk? True removed 567 files ===== Running in build: run configure.py ===== Running in build: save configure command ===== Running in build: Writing additional setup scripts for conda. ===== Running in build: libtbx.scons.bat ===== Running in build: libtbx.scons.bat ===== Running in build: rebuild rotarama ===== Running in build: rebuild cablam ===== Running in .: libtbx.refresh Bootstrap success: update, build None