14/03/2020 6:00:02.16 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 93605 100 93605 0 0 93605 0 0:00:01 --:--:-- 0:00:01 265k 14/03/2020 6:00:02.66 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 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 builder@cci.lbl.gov:jvgmry_annlib.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:jvgmry_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:k48ywv_ccp4io.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:k48ywv_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:ftvagr_eigen.tar.gz ===== Running in modules: getting remote file builder@cci.lbl.gov:ftvagr_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 7a3cb79a4..2ceb0e364 master -> origin/master * [new branch] bitshuffle -> origin/bitshuffle Updating 7a3cb79a4..2ceb0e364 Fast-forward .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 +- algorithms/integration/processor.py | 2 +- command_line/anvil_correction.py | 354 +++++++++++++++++++++ .../programs/dials_anvil_correction.rst | 52 +++ doc/sphinx/documentation/programs/index.rst | 1 + newsfragments/1090.feature | 2 + test/command_line/test_anvil_correction.py | 121 +++++++ test/command_line/test_cosym.py | 6 + util/phil.py | 19 +- 12 files changed, 548 insertions(+), 17 deletions(-) create mode 100644 command_line/anvil_correction.py create mode 100644 doc/sphinx/documentation/programs/dials_anvil_correction.rst create mode 100644 newsfragments/1090.feature create mode 100644 test/command_line/test_anvil_correction.py Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 1ed1507..b6b3275 master -> origin/master Updating 1ed1507..b6b3275 Fast-forward format/FormatCBFMultiTile.py | 5 ++++- format/FormatEigerStream.py | 5 ++--- format/cbf_writer.py | 19 ++++++++++++++++--- 3 files changed, 22 insertions(+), 7 deletions(-) Current branch master is up to date. Already up to date. Current branch master is up to date. svn: E155004: Run 'svn cleanup' to remove locks (type 'svn help cleanup' for details) svn: E155004: Working copy 'C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\ccp4io_adaptbx' locked. svn: E155004: 'C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\ccp4io_adaptbx' is already locked. ===== 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 Process failed with return code 1