Member Site › Forums › Rosetta 3 › Rosetta 3 – Build/Install › run unit test error
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Anonymous.
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August 24, 2013 at 8:06 pm #1701
Anonymous
python test/run.py -d /rosetta3.2/rosetta_database –mode=release UnitTestExecutable = [“protocols.test”, “core.test”, “ObjexxFCL.test”, “numeric.test”, “utility.test”, “apps.test”, “devel.test”] –mute=MUTE-all
I got following error:
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Paths: cd build/test/release/linux/3.5/32/x86/gcc/ && command line: ./apps.test –database /rosetta3.2/rosetta_database -mute MUTE-all
Running 1 test
Test suite: LigandDockTest (test/apps/public/ligand_docking/ligand_dock.cxxtest.hh)
core.init: Mini-Rosetta version exported from unknown
core.init: command: ./apps.test –database /rosetta3.2/rosetta_database -mute MUTE-all -run:constant_seed -run:rng mt19937 -in:file:s apps/public/ligand_docking/7cpa_7cpa_input.pdb -in:file:native apps/public/ligand_docking/7cpa_7cpa_native.pdb -out:path:pdb apps/public/ligand_docking -packing:no_optH -docking:randomize2 -docking:uniform_trans 5 -docking:ligand:start_from -1.731 32.589 -5.039 -docking:ligand:minimize_ligand -docking:ligand:harmonic_torsions 10
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
Warning: Unable to locate database file chemical/residue_type_sets/fa_standard
ERROR: Unable to open file: /rosetta3.2/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 96
Paths: cd build/test/release/linux/3.5/32/x86/gcc/ && command line: ./devel.test –database /rosetta3.2/rosetta_database -mute MUTE-all
bash: ./devel.test: No such file or directory
Unable to read yaml file with test results build/test/release/linux/3.5/32/x86/gcc//devel.test.yaml – unit test run aborted! -
August 24, 2013 at 9:56 pm #9235
Don’t mix Rosetta versions and database versions. No attempt at compatibility is attempted between the layout and contents of the Rosetta database between different versions. If you’re running the Rosetta 3.5 release applications, you should be using the Rosetta 3.5 release database. Trying to use the 3.2 database isn’t going to work, for any application, not just the unit tests.
P.S. the “./devel.test: No such file or directory” bit of things isn’t anything to worry about. The released version doesn’t have the “devel” library, and as such doesn’t have the devel tests. (But the test running script still tries to run them anyway.)
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August 25, 2013 at 10:54 am #9237
How can i remove Rosetta 3.5 completely from my system ??
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August 25, 2013 at 7:53 pm #9238
Rosetta doesn’t do any complex system settings changes by itself. If you want to uninstall it, all you have to do is delete the directory (or directories) where it was installed.
That said, because Rosetta stays in it’s own directories, there’s no reason you can’t have multiple versions of Rosetta simultaneously installed on a single machine. You just need to make sure that you’re using executable and database from the correct directory when you do runs.
That last bit is where you might be running into issues. If you have manually added a Rosetta directory to your $PATH variable, when you run something like “rosetta_scripts.linuxgccrelease”, you’ll get whichever version the command prompt autoresolves the command to. You won’t have that problem if you explicitly specify the directory (e.g. “/path/to/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease”). Likewise, if you specify the path to the database with an environment variable like $ROSETTA3_DB, that will only work with one version. If you manually specify it on the commandline with the “-d” flag, you can specify which version to use.
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