benedictpaten/sonLib — Issue #7: error in "make test"
Author: thirtyeggs
Created: 2011-10-12 02:20:38+00:00
State: open

Hi Benedict,

When I first ran "make test" I got many error massages like that:

```
.Running the command: sonLib_cigarTest /tmp/tmpKviSbo False
/bin/sh: sonLib_cigarTest: command not found
E......Running the command: sonLib_kvDatabaseTest --type=kyototycoon --host=localhost --port=1978
/bin/sh: sonLib_kvDatabaseTest: command not found
E.Running the command: sonLib_kvDatabaseTest --type=tokyocabinet
/bin/sh: sonLib_kvDatabaseTest: command not found
ERunning the command: sonLibTests DEBUG
/bin/sh: sonLibTests: command not found
E
======================================================================
ERROR: Tests consistency with C version of this function.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioioTest.py", line 165, in testFastaReadWriteC
system(command)
File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioio.py", line 160, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, i))
RuntimeError: Command: sonLib_fastaCTest /tmp/tmp0t00zf /tmp/tmpbVNOKW exited with non-zero status 32512
```
After adding sonLib/bin to $PATH manually, only following one error were remained:

```

======================================================================
ERROR: testSonLibKVKyotoTycoon (kvdbTest.TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/kvdbTest.py", line 22, in testSonLibKVKyotoTycoon
system("sonLib_kvDatabaseTest --type=kyototycoon --host=localhost --port=1978")
File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioio.py", line 160, in system
raise RuntimeError("Command: %s exited with non-zero status %i" % (command, i))
RuntimeError: Command: sonLib_kvDatabaseTest --type=kyototycoon --host=localhost --port=1978 exited with non-zero status 32768

----------------------------------------------------------------------
Ran 18 tests in 22.743s

```

Can I ask how I can remove it?
Thank you.

Yun