10/08/2019 6:00:01.45 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 14 91541 14 12938 0 0 12938 0 0:00:07 --:--:-- 0:00:07 59077 100 91541 100 91541 0 0 91541 0 0:00:01 --:--:-- 0:00:01 408k 10/08/2019 6:00:15.28 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base_tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q base_tmp\ & ) 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\ & ) The system cannot find the file specified. Performing actions: cleanup hot update base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_base_packages.py --python-shared --all --phenix --labelit --dials --xia2 --nproc=20 --skip-if-exists ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:fp76it_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:fp76it_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 ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:js6jzz_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:js6jzz_scons.tar.gz ===== Running in modules: delete remote temporary archive of scons ===== Running in modules: extracting archive files to scons ===== Running in modules: delete local temporary archive of scons ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:tinx11_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:tinx11_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 rdo20@cci.lbl.gov:szkmhx_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:szkmhx_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 2e607e7bb..72c93eab3 master -> origin/master Updating 2e607e7bb..72c93eab3 Fast-forward command_line/cosym.py | 3 +- command_line/plot_Fo_vs_Fc.py | 256 +++++++++++++++++++++ extensions/__init__.py | 6 +- ...dispersion_extended_spotfinder_threshold_ext.py | 23 +- extensions/dispersion_spotfinder_threshold_ext.py | 2 - test/command_line/test_export_best.py | 56 ++--- test/command_line/test_plot_Fo_vs_Fc.py | 13 ++ 7 files changed, 311 insertions(+), 48 deletions(-) create mode 100644 command_line/plot_Fo_vs_Fc.py create mode 100644 test/command_line/test_plot_Fo_vs_Fc.py Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx * [new branch] dxtbx-70 -> origin/dxtbx-70 * [new branch] extend-regression-tests -> origin/extend-regression-tests Already up to date. Current branch master is up to date. Updating 'ccp4io_adaptbx': At revision 143. Updating 'solve_resolve': At revision 1730. Updating 'clipper': At revision 19. Updating 'ksdssp': At revision 14. Updating 'phenix_regression': U phenix_regression\iotbx\tst_iotbx_reflection_file.csh Updated to revision 4643. Updating 'opt_resources': At revision 6. Updating 'phenix': U phenix\wxGUI2\SelectionEditor.py A phenix\phenix\pdb_tools\rama_z_score\process_molprobity_database.py Updated to revision 13011. 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. Cloning into 'cctbx_project'... 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Receiving objects: 89% (216644/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 90% (219078/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 91% (221513/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 92% (223947/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 93% (226381/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 94% (228815/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 95% (231249/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 96% (233684/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 97% (236118/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 98% (238552/243420), 85.82 MiB | 17.78 MiB/s Receiving objects: 99% (240986/243420), 90.34 MiB | 17.53 MiB/s remote: Total 243420 (delta 29), reused 40 (delta 20), pack-reused 243343 Receiving objects: 100% (243420/243420), 90.34 MiB | 17.53 MiB/s Receiving objects: 100% (243420/243420), 90.96 MiB | 11.29 MiB/s, done. Resolving deltas: 0% (0/192353) Resolving deltas: 1% (1925/192353) Resolving deltas: 2% (3853/192353) Resolving deltas: 3% (5783/192353) Resolving deltas: 4% (7707/192353) Resolving deltas: 5% (9633/192353) Resolving deltas: 5% (10530/192353) Resolving deltas: 6% (11597/192353) Resolving deltas: 7% (13473/192353) Resolving deltas: 8% (15421/192353) Resolving deltas: 9% (17326/192353) Resolving deltas: 10% (19246/192353) Resolving deltas: 10% (20977/192353) Resolving deltas: 11% (21168/192353) Resolving deltas: 12% (23089/192353) Resolving deltas: 13% (25036/192353) Resolving deltas: 14% (26940/192353) Resolving deltas: 15% (28854/192353) Resolving deltas: 15% (30711/192353) Resolving deltas: 16% (30792/192353) Resolving deltas: 17% (32720/192353) Resolving deltas: 18% (34628/192353) Resolving deltas: 19% (36575/192353) Resolving deltas: 20% (38483/192353) Resolving deltas: 21% (40401/192353) Resolving deltas: 21% (41260/192353) Resolving deltas: 22% (42329/192353) Resolving deltas: 23% (44247/192353) Resolving deltas: 24% (46170/192353) Resolving deltas: 25% (48094/192353) Resolving deltas: 26% (50031/192353) Resolving deltas: 26% (50576/192353) Resolving deltas: 27% (51997/192353) Resolving deltas: 28% (53873/192353) Resolving deltas: 29% (55789/192353) Resolving deltas: 30% (57713/192353) Resolving deltas: 30% (59395/192353) Resolving deltas: 31% (59634/192353) Resolving deltas: 32% (61584/192353) Resolving deltas: 33% (63477/192353) Resolving deltas: 34% (65496/192353) Resolving deltas: 35% (67367/192353) Resolving deltas: 35% (69165/192353) Resolving deltas: 36% (69254/192353) Resolving deltas: 37% (71231/192353) Resolving deltas: 38% (73144/192353) Resolving deltas: 39% (75019/192353) Resolving deltas: 39% (76516/192353) Resolving deltas: 40% (76947/192353) Resolving deltas: 41% (78913/192353) Resolving deltas: 42% (81320/192353) Resolving deltas: 43% (82741/192353) Resolving deltas: 43% (84408/192353) Resolving deltas: 44% (84663/192353) Resolving deltas: 45% (86656/192353) Resolving deltas: 46% (88485/192353) Resolving deltas: 47% (90408/192353) Resolving deltas: 48% (92515/192353) Resolving deltas: 49% (94257/192353) Resolving deltas: 50% (96342/192353) Resolving deltas: 51% (98133/192353) Resolving deltas: 51% (99836/192353) Resolving deltas: 52% (100060/192353) Resolving deltas: 53% (102281/192353) Resolving deltas: 54% (103918/192353) Resolving deltas: 55% (105837/192353) Resolving deltas: 56% (107749/192353) Resolving deltas: 56% (109395/192353) Resolving deltas: 57% (109778/192353) Resolving deltas: 58% (111590/192353) Resolving deltas: 59% (113491/192353) Resolving deltas: 60% (115438/192353) Resolving deltas: 61% (117394/192353) Resolving deltas: 61% (117695/192353) Resolving deltas: 62% (119290/192353) Resolving deltas: 63% (121308/192353) Resolving deltas: 64% (123127/192353) Resolving deltas: 65% (125045/192353) Resolving deltas: 65% (126194/192353) Resolving deltas: 66% (126998/192353) Resolving deltas: 67% (128947/192353) Resolving deltas: 68% (130804/192353) Resolving deltas: 69% (132727/192353) Resolving deltas: 69% (134298/192353) Resolving deltas: 70% (134682/192353) Resolving deltas: 71% (136583/192353) Resolving deltas: 72% (138501/192353) Resolving deltas: 73% (140436/192353) Resolving deltas: 74% (142438/192353) Resolving deltas: 74% (143069/192353) Resolving deltas: 75% (144302/192353) Resolving deltas: 76% (146211/192353) Resolving deltas: 77% (148143/192353) Resolving deltas: 78% (150064/192353) Resolving deltas: 78% (150612/192353) Resolving deltas: 79% (151998/192353) Resolving deltas: 80% (153909/192353) Resolving deltas: 81% (155866/192353) Resolving deltas: 82% (157810/192353) Resolving deltas: 82% (158458/192353) Resolving deltas: 83% (159663/192353) Resolving deltas: 84% (161637/192353) Resolving deltas: 85% (163544/192353) Resolving deltas: 86% (165431/192353) Resolving deltas: 86% (166608/192353) Resolving deltas: 87% (167375/192353) Resolving deltas: 88% (169274/192353) Resolving deltas: 89% (171196/192353) Resolving deltas: 90% (173125/192353) Resolving deltas: 90% (174701/192353) Resolving deltas: 91% (175048/192353) Resolving deltas: 92% (177020/192353) Resolving deltas: 93% (178937/192353) Resolving deltas: 94% (180850/192353) Resolving deltas: 94% (182661/192353) Resolving deltas: 95% (182737/192353) Resolving deltas: 96% (184662/192353) Resolving deltas: 97% (186587/192353) Resolving deltas: 98% (188517/192353) Resolving deltas: 99% (190434/192353) Resolving deltas: 99% (190534/192353) Resolving deltas: 100% (192353/192353) Resolving deltas: 100% (192353/192353), done. Checking out files: 4% (269/6172) Checking out files: 5% (309/6172) Checking out files: 6% (371/6172) Checking out files: 7% (433/6172) Checking out files: 8% (494/6172) Checking out files: 9% (556/6172) Checking out files: 9% (584/6172) Checking out files: 10% (618/6172) Checking out files: 11% (679/6172) Checking out files: 12% (741/6172) Checking out files: 13% (803/6172) Checking out files: 14% (865/6172) Checking out files: 15% (926/6172) Checking out files: 15% (985/6172) Checking out files: 16% (988/6172) Checking out files: 16% (1046/6172) Checking out files: 17% (1050/6172) Checking out files: 18% (1111/6172) Checking out files: 19% (1173/6172) Checking out files: 20% (1235/6172) Checking out files: 21% (1297/6172) Checking out files: 21% (1330/6172) Checking out files: 22% (1358/6172) Checking out files: 23% (1420/6172) Checking out files: 24% (1482/6172) Checking out files: 25% (1543/6172) Checking out files: 26% (1605/6172) Checking out files: 26% (1645/6172) Checking out files: 27% (1667/6172) Checking out files: 28% (1729/6172) Checking out files: 29% (1790/6172) Checking out files: 30% (1852/6172) Checking out files: 31% (1914/6172) Checking out files: 31% (1953/6172) Checking out files: 32% (1976/6172) Checking out files: 33% (2037/6172) Checking out files: 34% (2099/6172) Checking out files: 35% (2161/6172) Checking out files: 35% (2203/6172) Checking out files: 36% (2222/6172) Checking out files: 37% (2284/6172) Checking out files: 38% (2346/6172) Checking out files: 39% (2408/6172) Checking out files: 40% (2469/6172) Checking out files: 40% (2530/6172) Checking out files: 41% (2531/6172) Checking out files: 42% (2593/6172) Checking out files: 43% (2654/6172) Checking out files: 44% (2716/6172) Checking out files: 45% (2778/6172) Checking out files: 45% (2827/6172) Checking out files: 46% (2840/6172) Checking out files: 47% (2901/6172) Checking out files: 48% (2963/6172) Checking out files: 49% (3025/6172) Checking out files: 50% (3086/6172) Checking out files: 50% (3120/6172) Checking out files: 51% (3148/6172) Checking out files: 52% (3210/6172) Checking out files: 53% (3272/6172) Checking out files: 53% (3289/6172) Checking out files: 54% (3333/6172) Checking out files: 55% (3395/6172) Checking out files: 56% (3457/6172) Checking out files: 56% (3467/6172) Checking out files: 57% (3519/6172) Checking out files: 58% (3580/6172) Checking out files: 59% (3642/6172) Checking out files: 59% (3702/6172) Checking out files: 60% (3704/6172) Checking out files: 61% (3765/6172) Checking out files: 62% (3827/6172) Checking out files: 62% (3882/6172) Checking out files: 63% (3889/6172) Checking out files: 64% (3951/6172) Checking out files: 65% (4012/6172) Checking out files: 66% (4074/6172) Checking out files: 67% (4136/6172) Checking out files: 67% (4157/6172) Checking out files: 68% (4197/6172) Checking out files: 69% (4259/6172) Checking out files: 70% (4321/6172) Checking out files: 71% (4383/6172) Checking out files: 71% (4419/6172) Checking out files: 72% (4444/6172) Checking out files: 73% (4506/6172) Checking out files: 73% (4548/6172) Checking out files: 74% (4568/6172) Checking out files: 75% (4629/6172) Checking out files: 76% (4691/6172) Checking out files: 76% (4707/6172) Checking out files: 77% (4753/6172) Checking out files: 78% (4815/6172) Checking out files: 79% (4876/6172) Checking out files: 80% (4938/6172) Checking out files: 81% (5000/6172) Checking out files: 82% (5062/6172) Checking out files: 83% (5123/6172) Checking out files: 84% (5185/6172) Checking out files: 84% (5190/6172) Checking out files: 85% (5247/6172) Checking out files: 86% (5308/6172) Checking out files: 87% (5370/6172) Checking out files: 88% (5432/6172) Checking out files: 89% (5494/6172) Checking out files: 89% (5503/6172) Checking out files: 90% (5555/6172) Checking out files: 91% (5617/6172) Checking out files: 92% (5679/6172) Checking out files: 93% (5740/6172) Checking out files: 93% (5742/6172) Checking out files: 94% (5802/6172) Checking out files: 95% (5864/6172) Checking out files: 96% (5926/6172) Checking out files: 96% (5974/6172) Checking out files: 97% (5987/6172) Checking out files: 98% (6049/6172) Checking out files: 98% (6089/6172) Checking out files: 99% (6111/6172) Checking out files: 100% (6172/6172) Checking out files: 100% (6172/6172), done. f5fc0c1212632716d5212ddd9a9e4a1a2e86a72d Already up to date. Current branch master is up to date. Updating 'suitename': At revision 11. Already up to date. Current branch master is up to date. Updating 'chem_data': svn: warning: W205011: Error handling externals definition for 'chem_data\geostd': svn: warning: W170013: Unable to connect to a repository at URL 'https://svn.code.sf.net/p/geostd/code/trunk' At revision 321. svn: E205011: Failure occurred processing one or more externals definitions ===== Running in modules: extracting files from msgpack-3.1.1.tar.gz ===== Running in modules\dials: git pull --rebase ===== Running in modules: svn update probe --non-interactive --trust-server-cert ===== Running in modules: svn update reduce --non-interactive --trust-server-cert ===== Running in modules\dxtbx: git pull --rebase ===== Running in modules: svn update ccp4io_adaptbx --non-interactive --trust-server-cert ===== Running in modules: svn update solve_resolve --non-interactive --trust-server-cert ===== Running in modules: svn update clipper --non-interactive --trust-server-cert ===== Running in modules: svn update ksdssp --non-interactive --trust-server-cert ===== Running in modules: svn update phenix_regression --non-interactive --trust-server-cert ===== Running in modules: svn update opt_resources --non-interactive --trust-server-cert ===== Running in modules: svn update phenix --non-interactive --trust-server-cert ===== Running in modules: svn update Plex --non-interactive --trust-server-cert ===== Running in modules: svn update tntbx --non-interactive --trust-server-cert ===== Running in modules: svn update pulchra --non-interactive --trust-server-cert ===== Running in modules: svn update PyQuante --non-interactive --trust-server-cert ===== Running in modules\boost: git pull --rebase ===== Running in modules: git clone --recursive https://github.com/cctbx/cctbx_project.git cctbx_project --progress --verbose setting branch master to rebase ===== Running in modules\cctbx_project: git rev-parse HEAD ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Running in modules: svn update suitename --non-interactive --trust-server-cert ===== Running in modules\xia2: git pull --rebase ===== Running in modules: svn update chem_data --non-interactive --trust-server-cert Process failed with return code 1