Closed yurivict closed 1 year ago
Dear @yurivict,
Thanks very much for reporting these issues. I don't have a FreeBDS
test rig set up handy, so I am going to tag @stevenweaver who is much more skilled at cross-platform testing to see what the issue might be. I have an idea about what the first error might be, but really puzzled by the second.
Best, Sergei
Stale issue message
Not stale.
Dear @yurivict,
Should be resolved with version 2.5.43.
Best, Sergei
Hi Sergei,
2.5.43 still has the same 2 cases failing.
Yuri
Dear @yurivict,
Well, that was embarrassing. I forgot to merge the pull request fixing the issues before tagging off a 2.5.43. I've re-released 2.5.43 with the fixes included.
Sorry about this.
Best, Sergei
Now the test UNIT-TESTS
runs for over an hour and doesn't finish.
Is this normal?
Dear @yurivict,
Not normal. Unit tests should not take more than a second or two. I do not see this behavior with the 2.5.43 on the test system I have been using...
azureuser@FreeBSD:~/hyphy $ uname -a
FreeBSD FreeBSD 13.1-RELEASE-p3 FreeBSD 13.1-RELEASE-p3 GENERIC amd64
azureuser@FreeBSD:~/hyphy $ make test
Running tests...
Test project /usr/home/azureuser/hyphy
Start 1: UNIT-TESTS
1/20 Test #1: UNIT-TESTS ....................... Passed 1.96 sec
Start 2: CODON
2/20 Test #2: CODON ............................ Passed 1.50 sec
Start 3: PROTEIN
3/20 Test #3: PROTEIN .......................... Passed 10.20 sec
Start 4: MTCODON
4/20 Test #4: MTCODON .......................... Passed 36.58 sec
Start 5: ALGAE
5/20 Test #5: ALGAE ............................ Passed 12.45 sec
Start 6: CILIATES
6/20 Test #6: CILIATES ......................... Passed 23.62 sec
Start 7: SLAC
7/20 Test #7: SLAC ............................. Passed 4.12 sec
Start 8: SLAC-PARTITIONED
8/20 Test #8: SLAC-PARTITIONED ................. Passed 14.43 sec
Start 9: FEL
9/20 Test #9: FEL .............................. Passed 36.11 sec
Start 10: MEME
10/20 Test #10: MEME ............................. Passed 95.53 sec
Start 11: MEME-PARTITIONED
11/20 Test #11: MEME-PARTITIONED ................. Passed 76.79 sec
Start 12: BUSTED
12/20 Test #12: BUSTED ........................... Passed 25.77 sec
Start 13: BUSTED-SRV
13/20 Test #13: BUSTED-SRV ....................... Passed 26.28 sec
Start 14: RELAX
14/20 Test #14: RELAX ............................ Passed 56.22 sec
Start 15: FUBAR
15/20 Test #15: FUBAR ............................ Passed 0.65 sec
Start 16: BGM
16/20 Test #16: BGM .............................. Passed 3.68 sec
Start 17: CONTRAST-FEL
17/20 Test #17: CONTRAST-FEL ..................... Passed 101.03 sec
Start 18: GARD
18/20 Test #18: GARD ............................. Passed 0.09 sec
Start 19: FADE
19/20 Test #19: FADE ............................. Passed 5.12 sec
Start 20: ABSREL
20/20 Test #20: ABSREL ........................... Passed 40.08 sec
100% tests passed, 0 tests failed out of 20
Can you try
$bash run_unit_tests.sh
to see which individual unit test gets stuck?
Best, Sergei
$ bash run_unit_tests.sh
./tests/hbltests/UnitTests/HBLCommands/Abs.bf
./tests/hbltests/UnitTests/HBLCommands/Add.bf
./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf
./tests/hbltests/UnitTests/HBLCommands/Arctan.bf
./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf
./tests/hbltests/UnitTests/HBLCommands/Beta.bf
./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf
./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf
./tests/hbltests/UnitTests/HBLCommands/Branchname.bf
./tests/hbltests/UnitTests/HBLCommands/CChi2.bf
./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/Call.bf
./tests/hbltests/UnitTests/HBLCommands/Caret.bf
./tests/hbltests/UnitTests/HBLCommands/Category.bf
./tests/hbltests/UnitTests/HBLCommands/Columns.bf
./tests/hbltests/UnitTests/HBLCommands/Continue.bf
./tests/hbltests/UnitTests/HBLCommands/Cos.bf
./tests/hbltests/UnitTests/HBLCommands/DataSet.bf
./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf
./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf
./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf
./tests/hbltests/UnitTests/HBLCommands/Divide.bf
./tests/hbltests/UnitTests/HBLCommands/Do.bf
./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf
./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf
./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf
./tests/hbltests/UnitTests/HBLCommands/Erf.bf
./tests/hbltests/UnitTests/HBLCommands/Eval.bf
./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf
Check errors.log for execution error details.
./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf
./tests/hbltests/UnitTests/HBLCommands/Exp.bf
./tests/hbltests/UnitTests/HBLCommands/Export.bf
./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf
./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf
./tests/hbltests/UnitTests/HBLCommands/For.bf
./tests/hbltests/UnitTests/HBLCommands/Format.bf
./tests/hbltests/UnitTests/HBLCommands/Function.bf
./tests/hbltests/UnitTests/HBLCommands/Gamma.bf
./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf
./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf
./tests/hbltests/UnitTests/HBLCommands/GetString.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf
./tests/hbltests/UnitTests/HBLCommands/IBeta.bf
./tests/hbltests/UnitTests/HBLCommands/IGamma.bf
./tests/hbltests/UnitTests/HBLCommands/If.bf
./tests/hbltests/UnitTests/HBLCommands/Integrate.bf
./tests/hbltests/UnitTests/HBLCommands/Inverse.bf
./tests/hbltests/UnitTests/HBLCommands/JSON.bf
./tests/hbltests/UnitTests/HBLCommands/Join.bf
./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf
./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf
./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf
./tests/hbltests/UnitTests/HBLCommands/Log.bf
./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf
./tests/hbltests/UnitTests/HBLCommands/Max.bf
./tests/hbltests/UnitTests/HBLCommands/Min.bf
./tests/hbltests/UnitTests/HBLCommands/Model.bf
./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf
./tests/hbltests/UnitTests/HBLCommands/Random.bf
./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf
./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf
./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf
./tests/hbltests/UnitTests/HBLCommands/Return.bf
./tests/hbltests/UnitTests/HBLCommands/Rows.bf
./tests/hbltests/UnitTests/HBLCommands/Simplex.bf
./tests/hbltests/UnitTests/HBLCommands/Simplify.bf
./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf
./tests/hbltests/UnitTests/HBLCommands/Sin.bf
./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf
./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf
./tests/hbltests/UnitTests/HBLCommands/Subtract.bf
./tests/hbltests/UnitTests/HBLCommands/Tan.bf
./tests/hbltests/UnitTests/HBLCommands/Time.bf
./tests/hbltests/UnitTests/HBLCommands/TipCount.bf
./tests/hbltests/UnitTests/HBLCommands/TipName.bf
./tests/hbltests/UnitTests/HBLCommands/Topology.bf
./tests/hbltests/UnitTests/HBLCommands/Transpose.bf
./tests/hbltests/UnitTests/HBLCommands/Tree.bf
./tests/hbltests/UnitTests/HBLCommands/Type.bf
./tests/hbltests/UnitTests/HBLCommands/While.bf
./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf
./tests/hbltests/UnitTests/HBLCommands/assert.bf
./tests/hbltests/UnitTests/HBLCommands/break.bf
./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf
./tests/hbltests/UnitTests/HBLCommands/include.bf
./tests/hbltests/UnitTests/HBLCommands/lfunction.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf
./tests/hbltests/UnitTests/HBLCommands/namespace.bf
\n\n------------------------SUMMARY (Failed Tests)----------------------------\n
\n The following tests failed:
run_unit_tests.sh: line 35: ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf: Permission denied
\n The output of the failed tests is below: \n
--------------------------------------------------------------
[Running COVERAGE TEST '!']
Error:
Failed to parse '"Failed to return 1 when evaluating `!` on a valid path string (/bin/bash)"' with the following error: Constant expression inside `` did not evaluate to a string in the following context: '"<ERROR HERE>Failed to return 1 when ' in call to assert(!validPath==1, "Failed to return 1 when evaluating `!` on a valid path string (/bin/bash)");
Function call stack
1 : assert(!validPath==1, "Failed to return 1 when evaluating `!` on a valid path string (/bin/bash)");
-------
2 : result=runTest();
-------
3 : runATest();
-------
Check errors.log for execution error details.
\n
\n\n------------------------SUMMARY (Failed Tests)----------------------------\n
1 Tests Failed
of 101 Tests Run
/bin/bash
is not a valid path. bash should be always looked up with /usr/bin/env bash
.
Dear @yurivict,
You are 100% right. The hardcoded /bin/bash
should have never been there. I fixed this issue in the 2.5.43 tag by replacing /bin/bash
with a path that's guaranteed to exist. Therefore, I am a bit puzzled as to why you are still seeing this issue.
Best, Sergei
FreeBSD 13.1