Bootstrap build started on Tue Mar 19 22:26:03 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 47389 0 --:--:-- --:--:-- --:--:-- 48183 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 11 104k 11 12339 0 0 56467 0 0:00:01 --:--:-- 0:00:01 57125 100 104k 100 104k 0 0 456k 0 --:--:-- --:--:-- --:--:-- 460k 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. From https://gitlab.developers.cam.ac.uk/scm/haematology/readgroup/phasertng e6eea2f2..b6c36c91 master -> origin/master * [new tag] svnrev_1892_gitrev_1879 -> svnrev_1892_gitrev_1879 Updating e6eea2f2..b6c36c91 Fast-forward phasertng/voyager/riker.py | 1 - 1 file changed, 1 deletion(-) Already up to date. Already up to date. Already up to date. Already up to date. Already up to date. Already up to date. From https://github.com/cctbx/cctbx_project 930e0e809e..8021f8f6ae master -> origin/master + 10f1ddc53a...bb869055c3 ChimeraXSelectionViewer -> origin/ChimeraXSelectionViewer (forced update) Updating 930e0e809e..8021f8f6ae Fast-forward libtbx/phil/tst_interface.py | 8 +- mmtbx/geometry_restraints/geo_file_parsing.py | 3 +- mmtbx/geometry_restraints/tst_geo_file_parsing.py | 12 +- .../application/errors/error_modifier_mm24.py | 166 +++++++++++++++------ 4 files changed, 134 insertions(+), 55 deletions(-) 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. 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 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\ccp4io: git pull --rebase ===== Running in modules\tntbx: git pull --rebase ===== Running in modules\phaser_regression: git pull --rebase ===== Running in modules\phasertng: git pull --rebase ===== Running in modules\phaser: git pull --rebase ===== Running in modules\voyager_regression: git pull --rebase ===== Running in modules\ccp4io_adaptbx: git pull --rebase ===== Running in modules\reduce: git pull --rebase ===== Running in modules\phaser_voyager: git pull --rebase ===== Running in modules\annlib: 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\annlib_adaptbx: 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 removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhaserTNGVC2015\Current\modules, walk? True removed 573 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