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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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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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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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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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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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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