12/06/2020 6:00:01.93 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 206k 12/06/2020 6:00:02.59 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:dtfpnh_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:dtfpnh_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:pnehur_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:pnehur_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:x9ysk1_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:x9ysk1_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 06a5073e3..f876f15d0 master -> origin/master bb0cff96b..21c9bdb53 dependencies -> origin/dependencies 01058345e..bf9bf9e50 dependencies-boost -> origin/dependencies-boost * [new branch] dependencies-msgpack -> origin/dependencies-msgpack * [new branch] dependencies-scipy -> origin/dependencies-scipy 5d9381abe..3b947bf72 detect_blanks -> origin/detect_blanks b83e1fce8..63768655c dials-3.0 -> origin/dials-3.0 7f2513ce9..001d869c4 dials-next -> origin/dials-next * [new branch] python373839 -> origin/python373839 Updating 06a5073e3..f876f15d0 Fast-forward .conda-envs/dials_py36_linux-64.txt | 12 +- .conda-envs/dials_py36_osx-64.txt | 12 +- .conda-envs/linux.txt | 12 +- .conda-envs/macos.txt | 13 +- .travis.yml | 10 -- CHANGELOG.rst | 15 +++ algorithms/refinement/corrgram.py | 5 +- command_line/make_sphinx_html.py | 3 +- command_line/missing_reflections.py | 144 +++++++++++++++++++++ doc/sphinx/dials_tutorial_include.py | 5 +- .../programs/dials_missing_reflections.rst | 14 ++ doc/sphinx/documentation/programs/index.rst | 1 + newsfragments/1259.feature | 1 - newsfragments/1284.bugfix | 1 - newsfragments/1285.feature | 1 + test/command_line/test_missing_reflections.py | 65 ++++++++++ util/missing_reflections.py | 97 ++++++++++++++ util/test_missing_reflections.py | 52 ++++++++ 18 files changed, 420 insertions(+), 43 deletions(-) create mode 100644 command_line/missing_reflections.py create mode 100644 doc/sphinx/documentation/programs/dials_missing_reflections.rst delete mode 100644 newsfragments/1259.feature delete mode 100644 newsfragments/1284.bugfix create mode 100644 newsfragments/1285.feature create mode 100644 test/command_line/test_missing_reflections.py create mode 100644 util/missing_reflections.py create mode 100644 util/test_missing_reflections.py Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx e78b312..150397a master -> origin/master 6a70b8e..e3351c2 pilatus_multi_panel -> origin/pilatus_multi_panel Updating e78b312..150397a Fast-forward CHANGELOG.rst | 12 ++++++++++++ format/FormatSMVADSCSN442.py | 22 ++++++++++++++++++++-- format/nexus.py | 24 +++++++++++------------- newsfragments/176.bugfix | 1 - newsfragments/178.bugfix | 1 - tests/format/test_FormatHDF5EigerNearlyNexus.py | 21 +++++++++++++++++++++ 6 files changed, 64 insertions(+), 17 deletions(-) delete mode 100644 newsfragments/176.bugfix delete mode 100644 newsfragments/178.bugfix 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