branch: master 「№56548」
Commited by: Sergey Lyskov
GitHub commit link: 「f3d253581039314e」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 13:56:21

Adding printing of tests runtime to PyRosetta tests

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branch: master 「№56547」
Commited by: Sergey Lyskov
GitHub commit link: 「b907c7afa033f446」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 13:43:21

PyRosetta. Refactoring how debug build is done, moving it binaries in to separate dir.

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branch: master 「№56546」
Commited by: Rocco Moretti
GitHub commit link: 「17fe662b15266a6f」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 12:50:17

Options reorg: remove extra files confusing PyRosetta build

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branch: master 「№56545」
Commited by: Rocco Moretti
GitHub commit link: 「7cc8381f04edecd9」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 10:40:10

Better-er output capture on database tests. Also caputure stderr. Integration test changes: resource_database_locator and resource_database_tables commandfile

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branch: master 「№56544」
Commited by: Rocco Moretti
GitHub commit link: 「533d1ee67e16dbf4」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 10:20:27

Make update_options an always-run when compiling To avoid compilation problems when someone updated options_rosetta.py and forgets to run update_options.sh, add the running of update_options.sh to the compilation process, for both scons and cmake. It should no longer be necessary to run update_options.sh manually when you change options_rosetta.py (though it shouldn't hurt anytyhing if you still want to). The additional time added should be minimal (fraction of a second). In conjunction, remove the autogenerated files from being tracked with git, and fix a few places which depended on autogenerated files which were removed/changed. Tested compilation with both scons and cmake, and with a fresh checkout. No compilation issues seen locally. NOTE: If you have a compilation scheme that doesn't use our standard scons/cmake builds (or a non-compilation use that uses the autogenerated options files), you may need to add update_options.sh to your build scheme. (I have done this already for BuildDocs.sh and make_ctags.sh)

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branch: master 「№56543」
Commited by: Labonte
GitHub commit link: 「2fa368f4de4a6b20」
Difference from previous tested commit:  code diff
Commit date: 2014-03-19 08:16:12

reverting previous push (I'll log on to the test server and try this again later, but it seems GCC 4.4 gives different uninitialized warnings even on different individual machines.)

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branch: master 「№56542」
Commited by: Labonte
GitHub commit link: 「ce1d0f723ecdc8f7」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 23:32:59

Warnings Removal: giving GCC 4.4 release another go with full Werror

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branch: master 「№56541」
Commited by: sarel
GitHub commit link: 「2137eff80d1442cc」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 12:55:49

not again... git is fast forwarding some changes. Repeating my earlier commit message: I'm removing warnings from the graphics viewer build. no changes expected. Merge branch 'master' of github.com:RosettaCommons/main

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branch: master 「№56540」
Commited by: Rocco Moretti
GitHub commit link: 「c8f19b3707584fe2」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 12:47:13

Better output capture on database tests. Hopefully will point to the issue with debug-mode resource_database_tables test on the server. Integration tests changes: resource_database_locator and resource_database_tables, with additional output information.

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branch: master 「№56539」
Commited by: Rocco Moretti
GitHub commit link: 「017f98a01650ec41」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 12:01:19

Hopefully fix gcc4.4 uninitialized variable isse in LeeRichards.cc

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branch: master 「№56538」
Commited by: Rocco Moretti
GitHub commit link: 「b0b6ebd5542f8a37」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 11:44:07

Fix unused variable issue with SymmetryInfo

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branch: master 「№56537」
Commited by: Tim Jacobs
GitHub commit link: 「3c58bcd7f83a5d03」
Difference from previous tested commit:  code diff
Commit date: 2014-03-18 11:12:19

Fixing a recently introduced error in LayeredDesign that broke the build.

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branch: master 「№56536」
Commited by: Frank DiMaio
GitHub commit link: 「b8d1b11ac6c35e38」
Difference from previous tested commit:  code diff
Commit date: 2014-03-17 22:43:35

merge master: Updating symmetryinfo so all information is saved/restored when reading/writing to a silent file.

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branch: master 「№56535」
Commited by: sboyken
GitHub commit link: 「d32256199abeda3e」
Difference from previous tested commit:  code diff
Commit date: 2014-03-17 22:20:09

Fixing clang/Xcode compiler linking error; clang/Xcode should now build fine To have things link properly in Xcode, I had to add the following include to protocols/outputter/SilentFileOutputter.cc: #include <core/io/silent/ProteinSilentStruct.tmpl.hh> //sboyken, 03/17/14 needed for proper linking in Xcode # ---------------------------------------- No changes to integration/unit tests This commit should fix linking errors for clang/Xcode that some have mentioned recently

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branch: master 「№56534」
Commited by: Labonte
GitHub commit link: 「2758cee2408d7e29」
Difference from previous tested commit:  code diff
Commit date: 2014-03-17 22:12:10

Warnings Removal: 14 uninitializeds from GCC 4.4 release mode

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branch: master 「№56533」
Commited by: Javier Castellanos
GitHub commit link: 「b6b55e0b1b2231a4」
Difference from previous tested commit:  code diff
Commit date: 2014-03-17 21:43:34

Fix to LayerDesign parsing of CombinedTasks

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