07/07/2020 6:00:01.80 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 99218 100 99218 0 0 99218 0 0:00:01 --:--:-- 0:00:01 129k 07/07/2020 6:00:02.67 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\ & ) The system cannot find the file specified. 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 ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_regression will be downloaded. ******************************************************************************* ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_examples will be downloaded. ******************************************************************************* 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:fk6fin_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:fk6fin_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:bbjsmt_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:bbjsmt_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:lwusuc_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:lwusuc_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 ba5ab53a1..cf0306831 master -> origin/master 8f33dfeee..8d758451f dials-3.0 -> origin/dials-3.0 d673882d4..3719ac31b dials-next -> origin/dials-next 2d09476b9..a3a419810 dials-next-2.2 -> origin/dials-next-2.2 * [new branch] hide-scale-stack-trace -> origin/hide-scale-stack-trace ed737807f..ae681c05d integration-output-people-numbers -> origin/integration-output-people-numbers + 866b24aae...c5d1c3486 python3738 -> origin/python3738 (forced update) * [new branch] resolutionizer-refactor -> origin/resolutionizer-refactor Updating ba5ab53a1..cf0306831 Fast-forward .azure-pipelines.yml | 2 +- .azure-pipelines/unix-build.yml | 18 +- .conda-envs/dials_py36_linux-64.txt | 2 +- .conda-envs/dials_py36_osx-64.txt | 2 +- .conda-envs/linux.txt | 2 +- .conda-envs/macos.txt | 2 +- CHANGELOG.rst | 17 + README.md | 2 +- algorithms/scaling/plots.py | 2 +- installer/bootstrap.py | 907 +++++++++++++++++++----------------- newsfragments/1274.bugfix | 1 - newsfragments/1277.feature | 1 - newsfragments/1279.bugfix | 1 - newsfragments/1320.misc | 7 + newsfragments/1322.misc | 1 + report/plots.py | 3 +- report/test_plots.py | 17 +- test/util/test_log.py | 3 +- util/log.py | 2 +- util/options.py | 6 +- 20 files changed, 539 insertions(+), 459 deletions(-) delete mode 100644 newsfragments/1274.bugfix delete mode 100644 newsfragments/1277.feature delete mode 100644 newsfragments/1279.bugfix create mode 100644 newsfragments/1320.misc create mode 100644 newsfragments/1322.misc Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx * [new branch] detector-housekeeping -> origin/detector-housekeeping 264b411..95d94a4 dls-eiger-0xffff -> origin/dls-eiger-0xffff 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. There is no tracking information for the current branch. Please specify which branch you want to rebase against. See git-pull(1) for details. git pull If you wish to set tracking information for this branch you can do so with: git branch --set-upstream-to=origin/ master ===== 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\amber_library: git pull --rebase ===== Running in modules: svn update ccp4io_adaptbx --non-interactive --trust-server-cert ===== Running in modules\solve_resolve: git pull --rebase Process failed with return code 1