make test error

[tallnuttcsiro]

Get this error with make test. Also python can't find the modules.
.../bin/sh: 1: sonLib_kvDatabaseTest: not found
E/bin/sh: 1: sonLibTests: not found

E

ERROR: testFastaReadWriteC (bioioTest.TestCase)

Tests consistency with C version of this function.

Traceback (most recent call last):
File "/OSM/HOME-MEL/all29c/bin/sonLib/bioioTest.py", line 185, in testFastaReadWriteC
system(command)
File "/OSM/HOME-MEL/all29c/bin/sonLib/bioio.py", line 185, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLib_fastaCTest /tmp/tmp8537yf /tmp/tmpG6V7Df exited with non-zero status 127

ERROR: testCigarReadWrite (cigarsTest.TestCase)

Tests the C code for reading and writing cigars against the python parser for cigars.

Traceback (most recent call last):
File "/OSM/HOME-MEL/all29c/bin/sonLib/cigarsTest.py", line 57, in testCigarReadWrite
system(command)
File "/OSM/HOME-MEL/all29c/bin/sonLib/bioio.py", line 185, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLib_cigarTest /tmp/tmpBZs1ok True exited with non-zero status 127

ERROR: testSonLibKVTokyoCabinet (kvdbTest.TestCase)

Traceback (most recent call last):
File "/OSM/HOME-MEL/all29c/bin/sonLib/kvdbTest.py", line 18, in testSonLibKVTokyoCabinet
system("sonLib_kvDatabaseTest --type=tokyocabinet")
File "/OSM/HOME-MEL/all29c/bin/sonLib/bioio.py", line 185, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLib_kvDatabaseTest --type=tokyocabinet exited with non-zero status 127

ERROR: testSonLibCTests (main.TestCase)

Run m,ost the sonLib CuTests, fail if any of them fail.

Traceback (most recent call last):
File "allTests.py", line 30, in testSonLibCTests
system("sonLibTests %s" % getLogLevelString())
File "/OSM/HOME-MEL/all29c/bin/sonLib/bioio.py", line 185, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLibTests CRITICAL exited with non-zero status 127

---

Ran 19 tests in 20.710s

FAILED (errors=4)
make: *** [test] Error 4

[ambarrio]

Got exactly the same error than @tallnuttcsiro

The sonLib_kvDatabaseTest program is there. The C function fails.

Any ideas?

[rfitak]

I also received the same errors as above. In the Makefile, I changed:

PYTHONPATH=.. PATH=../../bin:$$PATH python allTests.py --testLength=SHORT --logLevel=CRITICAL
to
PYTHONPATH=.. PATH=./bin:$$PATH python allTests.py --testLength=SHORT --logLevel=CRITICAL

This fixed the problem above with not finding certain executables. I am not sure why that particular path to "bin" was chosen. However, I have now run into another problem with the tests when running "make test". Here is the end of the output produced now from "make test":

OK (158 tests)

.

ERROR: testSonLibKVTokyoCabinet (kvdbTest.TestCase)

Traceback (most recent call last):
File "/hpchome/biodept/frr6/LASTZ/MAFTOOLS/sonLib/kvdbTest.py", line 18, in testSonLibKVTokyoCabinet
system("sonLib_kvDatabaseTest --type=tokyocabinet")
File "/hpchome/biodept/frr6/LASTZ/MAFTOOLS/sonLib/bioio.py", line 185, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLib_kvDatabaseTest --type=tokyocabinet exited with non-zero status 128

---

Ran 19 tests in 78.278s

FAILED (errors=1)
make: *** [test] Error 1

At least now I am only down to 1 error. Any ideas?

[awohns]

I'm having a similar issue. Did anyone ever resolve this error?

[Summer1019]

similar issue. Did this problem be solved?

[bioinformaticspcj]

I am also meeting the same problem. Did this problem be solved ?

[yuzhenpeng]

I am also meeting the same problem. Did this problem be solved ?

[diekhans]

what happens if you run
sonLib_kvDatabaseTest --type=tokyocabinet

by hand

[yuzhenpeng]

I get it as follow.
`
$sonLib_kvDatabaseTest --type=tokyocabinet

running Tokyo Cabinet sonLibKVDatabase tests

Running test case readWriteAndRemoveRecords

Exception: ST_KV_DATABASE_EXCEPTION: requested Tokyo Cabinet database, however s onlib is not compiled with Tokyo Cabinet support
Uncaught exception

`
@diekhans

[diekhans]

sonlib needs to be recompiled making sure it picks up tokyo cabinet and Kyoto Tycoon .

see sonLib/include.mk for how it checks for the library and header locations

Hi there,
I also get this error with the command "make test". Is there anyway to solve this? Thanks

ok
testSonLibKTTests (main.TestCase)
Run the sonLib KyotoTycoon interface tests. ... skipped 'ktserver command is missing'
testSonLibKVTokyoCabinet (main.TestCase)
Run the sonLib TokyoCabinet interface tests. ... running Tokyo Cabinet sonLibKVDatabase tests
Running test case readWriteAndRemoveRecords
Exception: ST_KV_DATABASE_EXCEPTION: requested Tokyo Cabinet database, however sonlib is not compiled with Tokyo Cabinet support
Uncaught exception
ERROR
testSonLibRedisTests (main.TestCase)
Run the sonLib Redis interface tests. ... skipped 'hiredis pkg-config package is missing'

======================================================================
ERROR: testSonLibKVTokyoCabinet (main.TestCase)
Run the sonLib TokyoCabinet interface tests.

Traceback (most recent call last):
File "allTests.py", line 75, in testSonLibKVTokyoCabinet
system("sonLib_kvDatabaseTest --type=tokyocabinet")
File "/data/gpfs/projects/punim0586/lecook/chipseq-pipeline/cross_species/bin/sonLib/src/sonLib/bioio.py", line 194, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: sonLib_kvDatabaseTest --type=tokyocabinet exited with non-zero status 128

---

Ran 19 tests in 73.614s

FAILED (errors=1, skipped=2)
make: *** [test] Error 1