11/05/2020 6:00:02.52 Get 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 95703 100 95703 0 0 95703 0 0:00:01 --:--:-- 0:00:01 206k 11/05/2020 6:00:05.60 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\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\PhenixVC2008\x64\Current>((ROBOCOPY empty build /MIR /COPYALL 1>nul ) & rmdir /S /Q build\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty conda_base /MIR /COPYALL 1>nul ) & rmdir /S /Q conda_base\ & ) Performing actions: cleanup hot update base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=phenix --install_conda --python=27 ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Running in modules: create remote temporary archive builder@cci.lbl.gov:kajqzu_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:kajqzu_annlib.tar.gz ===== Running in modules: delete remote temporary archive of annlib ===== Running in modules: extracting archive files to annlib ===== Running in modules: delete local temporary archive of annlib Existing non-git directory -- don't know what to do. skipping: scons ===== Running in modules: create remote temporary archive builder@cci.lbl.gov:nyuikl_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:nyuikl_ccp4io.tar.gz ===== Running in modules: delete remote temporary archive of ccp4io ===== Running in modules: extracting archive files to ccp4io ===== Running in modules: delete local temporary archive of ccp4io ===== Running in modules: create remote temporary archive builder@cci.lbl.gov:l9jbwj_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:l9jbwj_eigen.tar.gz ===== Running in modules: delete remote temporary archive of eigen ===== Running in modules: extracting archive files to eigen ===== Running in modules: delete local temporary archive of eigen ===== Downloading https://gitcdn.xyz/repo/dials/dependencies/dials-1.13/msgpack-3.1.1.tar.gz: 484 kB From https://github.com/dials/dials 5e26043ab..41e60a824 master -> origin/master 0cad16796..73c2de440 dials-next -> origin/dials-next * [new branch] dials-next-2.2 -> origin/dials-next-2.2 Updating 5e26043ab..41e60a824 Fast-forward algorithms/indexing/symmetry.py | 1 + algorithms/indexing/test_symmetry.py | 13 +++++++++++++ 2 files changed, 14 insertions(+) Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. Updating 'ccp4io_adaptbx': At revision 143. Updating 'solve_resolve': At revision 1752. Updating 'clipper': At revision 19. Updating 'ksdssp': At revision 14. Updating 'phenix_regression': At revision 4802. Updating 'opt_resources': At revision 6. Updating 'phenix': At revision 13609. Updating 'Plex': At revision 8. Updating 'tntbx': At revision 50. Updating 'pulchra': At revision 8. Updating 'PyQuante': At revision 25. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. Cloning into 'cctbx_project'... 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Receiving objects: 0% (1/253784) Receiving objects: 1% (2538/253784) Receiving objects: 2% (5076/253784), 756.01 KiB | 1.47 MiB/s Receiving objects: 3% (7614/253784), 756.01 KiB | 1.47 MiB/s Receiving objects: 3% (8549/253784), 1.70 MiB | 1.69 MiB/s Receiving objects: 4% (10152/253784), 1.70 MiB | 1.69 MiB/s Receiving objects: 5% (12690/253784), 1.70 MiB | 1.69 MiB/s Receiving objects: 6% (15228/253784), 2.64 MiB | 1.76 MiB/s Receiving objects: 7% (17765/253784), 2.64 MiB | 1.76 MiB/s Receiving objects: 7% (18373/253784), 3.56 MiB | 1.78 MiB/s Receiving objects: 8% (20303/253784), 3.56 MiB | 1.78 MiB/s Receiving objects: 9% (22841/253784), 3.56 MiB | 1.78 MiB/s Receiving objects: 10% (25379/253784), 4.53 MiB | 1.81 MiB/s Receiving objects: 11% (27917/253784), 4.53 MiB | 1.81 MiB/s Receiving objects: 11% (28277/253784), 5.51 MiB | 1.83 MiB/s Receiving objects: 12% (30455/253784), 5.51 MiB | 1.83 MiB/s Receiving objects: 13% (32992/253784), 6.49 MiB | 1.85 MiB/s Receiving objects: 14% (35530/253784), 6.49 MiB | 1.85 MiB/s Receiving objects: 15% (38068/253784), 17.15 MiB | 4.28 MiB/s Receiving objects: 15% (38276/253784), 17.15 MiB | 4.28 MiB/s Receiving objects: 16% (40606/253784), 17.15 MiB | 4.28 MiB/s Receiving objects: 17% (43144/253784), 17.15 MiB | 4.28 MiB/s Receiving objects: 18% (45682/253784), 25.87 MiB | 5.75 MiB/s Receiving objects: 18% (47433/253784), 35.64 MiB | 7.76 MiB/s Receiving objects: 19% (48219/253784), 35.64 MiB | 7.76 MiB/s Receiving objects: 20% (50757/253784), 35.64 MiB | 7.76 MiB/s Receiving objects: 21% (53295/253784), 35.64 MiB | 7.76 MiB/s Receiving objects: 22% (55833/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 23% (58371/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 24% (60909/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 25% (63446/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 26% (65984/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 27% (68522/253784), 44.32 MiB | 9.47 MiB/s Receiving objects: 28% 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objects: 43% (109128/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 44% (111665/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 45% (114203/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 46% (116741/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 47% (119279/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 48% (121817/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 49% (124355/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 50% (126892/253784), 64.79 MiB | 13.61 MiB/s Receiving objects: 51% (129430/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 52% (131968/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 53% (134506/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 54% (137044/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 54% (137967/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 55% (139582/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 56% (142120/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 57% (144657/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 58% (147195/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 59% (149733/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 60% (152271/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 61% (154809/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 62% (157347/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 63% (159884/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 64% (162422/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 65% (164960/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 66% (167498/253784), 75.82 MiB | 15.84 MiB/s Receiving objects: 67% (170036/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 68% (172574/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 69% (175111/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 70% (177649/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 71% (180187/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 72% (182725/253784), 84.98 MiB | 17.66 MiB/s Receiving objects: 73% 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Receiving objects: 89% (225868/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 89% (226574/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 90% (228406/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 91% (230944/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 92% (233482/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 93% (236020/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 94% (238557/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 95% (241095/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 96% (243633/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 97% (246171/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 98% (248709/253784), 91.08 MiB | 18.80 MiB/s Receiving objects: 99% (251247/253784), 94.93 MiB | 17.28 MiB/s remote: Total 253784 (delta 53), reused 57 (delta 33), pack-reused 253675 Receiving objects: 100% (253784/253784), 94.93 MiB | 17.28 MiB/s Receiving objects: 100% (253784/253784), 96.45 MiB | 11.21 MiB/s, done. 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Current branch master is up to date. Updating 'suitename': At revision 11. From https://github.com/xia2/xia2 * [new branch] dials-next-2.2 -> origin/dials-next-2.2 Already up to date. Current branch master is up to date. Updating 'chem_data': Fetching external item into 'chem_data\geostd': External at revision 213. At revision 339. X chem_data\geostd Performing status on external item at 'chem_data\geostd': Already up to date. Current branch master is up to date. warning: redirecting to https://git.uis.cam.ac.uk/cimr-phaser/phaser_regression.git/ Already up to date. Current branch master is up to date. Updating 'phenix_examples': At revision 150. Updating 'reel': At revision 265. Updating 'phenix_html': At revision 1471. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. Updating 'labelit': At revision 2088. Updating 'elbow': At revision 3837. Updating 'muscle': At revision 10. Updating 'gui_resources': At revision 59. Base conda installation: C:\Users\phaserbuilder\PhenixTestBuilds\phasertng\mc3 Installing phenix environment with: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\conda_envs\phenix_py27_win-64.txt Completed installation into: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base Python: 2.7.15 "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\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: True Boost threads enabled: True Enable CUDA: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build Top-down list of all modules involved: iota "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\iota" xia2 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\xia2" dials "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\dials" xfel "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel" prime "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\prime" simtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\simtbx" cma_es "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cma_es" amber_adaptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\amber_adaptbx" labelit "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\labelit" rstbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\rstbx" spotfinder "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\spotfinder" annlib+adaptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\annlib" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\annlib_adaptbx" phenix_examples "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples" phenix "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix" reel "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\reel" phaser "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phaser" phaser_regression "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phaser_regression" tntbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\tntbx" solve_resolve "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\solve_resolve" muscle "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\muscle" ksdssp "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\ksdssp" pulchra "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\pulchra" phenix_html "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html" phenix_regression "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression" elbow "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow" Plex "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\Plex" PyQuante "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\PyQuante" chem_data "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\chem_data" wxtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\wxtbx" gltbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\gltbx" mmtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx" suitename "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\suitename" king "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\king" probe "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\probe" reduce "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\reduce" crys3d "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\crys3d" dxtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\dxtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\ucif" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" cctbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\fable" omptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\boost" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\fable\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\dxtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\crys3d\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\reduce\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\probe\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\king\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\suitename\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\gltbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\wxtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\ksdssp\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\muscle\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\solve_resolve\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phaser_regression\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phaser\phaser\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\reel\reel\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix\phenix\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\spotfinder\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\rstbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\labelit\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\amber_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\simtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\prime\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\ui\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\cxi\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\clustering\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\merging\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\small_cell\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\dials\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\xia2\command_line" ================================================================================ WARNING: Can not find conda package in your environment You will have to keep track of dependencies yourself ================================================================================ Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\libtbx_refresh.py" Generating C++ header files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\include\scitbx\array_family" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\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 creating libtbx.scitbx.egg-info writing libtbx.scitbx.egg-info\PKG-INFO writing top-level names to libtbx.scitbx.egg-info\top_level.txt writing dependency_links to libtbx.scitbx.egg-info\dependency_links.txt writing entry points to libtbx.scitbx.egg-info\entry_points.txt writing manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' reading manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' writing manifest file 'libtbx.scitbx.egg-info\SOURCES.txt' Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\cctbx\eltbx" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\include\cctbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\libtbx_refresh.py" Copying to lib: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cbflib\pycbf\pycbf.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\include\smtbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\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\phenixvc2008\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 FormatEigerStream based on ['FormatMultiImage', 'Format'] found FormatGatanDM4 based on ['FormatMultiImage', 'Format'] found FormatHDF5 based on ['FormatMultiImage', 'Format'] 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 FormatNexusJungfrauHack based on ['FormatNexus'] 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 FormatSMVADSCSN442 based on ['FormatSMVADSCSN'] 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 running egg_info creating libtbx.dxtbx.egg-info writing libtbx.dxtbx.egg-info\PKG-INFO writing top-level names to libtbx.dxtbx.egg-info\top_level.txt writing dependency_links to libtbx.dxtbx.egg-info\dependency_links.txt writing entry points to libtbx.dxtbx.egg-info\entry_points.txt writing manifest file 'libtbx.dxtbx.egg-info\SOURCES.txt' reading manifest file 'libtbx.dxtbx.egg-info\SOURCES.txt' writing manifest file 'libtbx.dxtbx.egg-info\SOURCES.txt' Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\crys3d\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\reduce\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\probe\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\gltbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\gltbx" fonts: 8x13 9x15 10x20 Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\solve_resolve\libtbx_refresh.py" Number of hpp files generated from resolve cpp files: 721 Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\annlib_adaptbx\libtbx_refresh.py" Generating C++ files for self-inclusive approximate nearest neighbour Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\xfel\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\dials\libtbx_refresh.py" Updating entry points for dials 6 entries for entry point dials.integration.background 1 entries for entry point dials.integration.centroid 2 entries for entry point dials.spotfinder.threshold 3 entries for entry point dials.index.basis_vector_search 4 entries for entry point dxtbx.scaling_model_ext 1 entries for entry point dials.index.lattice_search 1 entries for entry point dxtbx.profile_model running egg_info creating libtbx.dials.egg-info writing libtbx.dials.egg-info\PKG-INFO writing top-level names to libtbx.dials.egg-info\top_level.txt writing dependency_links to libtbx.dials.egg-info\dependency_links.txt writing entry points to libtbx.dials.egg-info\entry_points.txt writing manifest file 'libtbx.dials.egg-info\SOURCES.txt' reading manifest file 'libtbx.dials.egg-info\SOURCES.txt' writing manifest file 'libtbx.dials.egg-info\SOURCES.txt' DIALS 2.dev.1572-g41e60a824 Identified autocompletable commands: dials.find_spots dials.geometry_viewer dials.index dials.integrate dials.reciprocal_lattice_viewer dials.refine dials.reindex dials.rl_png Installing autocompletion script into: Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\xia2\libtbx_refresh.py" XIA2 0.6.504-g6ae4695a Processing: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\iota\libtbx_refresh.py" running develop running egg_info writing src\iota.egg-info\PKG-INFO writing top-level names to src\iota.egg-info\top_level.txt writing dependency_links to src\iota.egg-info\dependency_links.txt writing entry points to src\iota.egg-info\entry_points.txt reading manifest file 'src\iota.egg-info\SOURCES.txt' writing manifest file 'src\iota.egg-info\SOURCES.txt' running build_ext Creating c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\conda_base\lib\site-packages\iota.egg-link (link to src) Adding iota 0.1 to easy-install.pth file Installing iota.filter_pickles-script.py script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.filter_pickles.exe script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.run-script.py script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.run.exe script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.track_images-script.py script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.track_images.exe script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota-script.py script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.exe script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.single_image-script.py script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installing iota.single_image.exe script to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\Scripts Installed c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\iota\src Processing dependencies for iota==0.1 Finished processing dependencies for iota==0.1 Done. Base conda installation: C:\Users\phaserbuilder\PhenixTestBuilds\phasertng\mc3 conda_setpaths.bat has been written successfully. conda_unsetpaths.bat has been written successfully. scons: Reading SConscript files ...