Dear Galaxy devs,
We are in the process of deploying Galaxy internally here at AgResearch, and I
am currently installing required dependencies. My question relates to RPy. It
seems that RPy2 is not yet supported by Galaxy, so we're stuck with RPy 1.0.3a,
and this seems to have rusted quite badly. (I note however that the remarks
previously made on the Galaxy lists about changes required to RPy appear to
have been rolled into 1.0.3a.)
After installing RPy 1.0.3a, I ran the bundled test suite. Many tests succeed,
but there are several errors, in the following categories:
1. Errors about numpy, e.g. object of type numpy.int64 has no len() (Maybe
numpy has changed since RPy 1.0.3a was written. I am using numpy 1.4.1 on
CentOS 6.)
2. Errors due to missing files, e.g. logit.r and table.txt test data files do
not appear to ship with RPy-1.0.3a (!)
3. An error in testLapackLoad, which may be because of (2), I'm not sure yet.
4. An R object index out of range error in testGetItemSlice, which looks quite
serious.
So here's my question. Just how much of RPy has to work, for its use in Galaxy
to be OK?
I attach my RPy test suite output in case anyone is (a) interested, (b) has any
useful comments.
cheers,
Simon
Simon Guest
Senior UNIX Technical Consultant
AgResearch, NZ
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=======================================================================
impulsive$ python testall.py --random
Modules to be tested: ['test_io.py', 'test_boolean.py', 'test_util.py',
'test_lapack_load.py', 'test_array.py', 'test_cleanup.py', 'test_topy.py',
'test_tor.py', 'test_vars.py', 'test_modes.py', 'test_numeric.py',
'test_init.py', 'test_noninteractive.py', 'test_robj.py', 'test_sigint.py']
Testing: test_topy
..Warning message:
In file(file, "rt") :
cannot open file 'table.txt': No such file or directory
E..................
======================================================================
ERROR: testDataFrameToList (test_topy.TypeConversionToPyTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_topy.py", line 65, in
testDataFrameToList
assert(r.read_table('table.txt', header=1) ==
RPy_RException: Error in file(file, "rt") : cannot open the connection
----------------------------------------------------------------------
Ran 21 tests in 0.027s
FAILED (errors=1)
Testing: test_boolean
..
----------------------------------------------------------------------
Ran 2 tests in 0.000s
OK
Testing: test_numeric
.E.E.E...E.E.E..............
======================================================================
ERROR: test16BitIntScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
229, in test16BitIntScalar
b = r.c(a[0])
TypeError: object of type 'numpy.int16' has no len()
======================================================================
ERROR: test32BitFloatScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
268, in test32BitFloatScalar
b = r.c(a[0])
TypeError: object of type 'numpy.float32' has no len()
======================================================================
ERROR: test32BitIntScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
219, in test32BitIntScalar
b = r.c(a[0])
TypeError: object of type 'numpy.int32' has no len()
======================================================================
ERROR: test64BitIntScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
209, in test64BitIntScalar
b = r.c(a[0])
TypeError: object of type 'numpy.int64' has no len()
======================================================================
ERROR: test8BitIntScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
239, in test8BitIntScalar
b = r.c(a[0])
TypeError: object of type 'numpy.int8' has no len()
======================================================================
ERROR: testBoolScalar (test_numeric.ArrayTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_numeric.py", line
250, in testBoolScalar
b = r.c(a[0])
TypeError: object of type 'numpy.bool_' has no len()
----------------------------------------------------------------------
Ran 28 tests in 0.052s
FAILED (errors=6)
Testing: test_modes
............
----------------------------------------------------------------------
Ran 12 tests in 0.029s
OK
Testing: test_lapack_load
Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'logit.r': No such file or directory
E
======================================================================
ERROR: testLapackLoad (test_lapack_load.LapackLoadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_lapack_load.py", line
20, in testLapackLoad
r.source(fi)
RPy_RException: Error in file(filename, "r", encoding = encoding) :
cannot open the connection
----------------------------------------------------------------------
Ran 1 test in 0.019s
FAILED (errors=1)
Testing: test_array
.......
----------------------------------------------------------------------
Ran 7 tests in 0.272s
OK
Testing: test_sigint
.
----------------------------------------------------------------------
Ran 1 test in 0.000s
OK
Testing: test_noninteractive
.
----------------------------------------------------------------------
Ran 1 test in 1.383s
OK
Testing: test_io
......
----------------------------------------------------------------------
Ran 6 tests in 0.428s
OK
Testing: test_tor
...........Warning message:
In .Primitive("log")(-1L) : NaNs produced
...
----------------------------------------------------------------------
Ran 14 tests in 0.005s
OK
Testing: test_util
...
----------------------------------------------------------------------
Ran 3 tests in 0.005s
OK
Testing: test_vars
.
----------------------------------------------------------------------
Ran 1 test in 0.001s
OK
Testing: test_init
.
----------------------------------------------------------------------
Ran 1 test in 0.000s
OK
Testing: test_robj
.......E.......
======================================================================
ERROR: testGetItemSlice (test_robj.RobjTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/guestsi/rpmbuild/BUILD/rpy-1.0.3/tests/test_robj.py", line 38, in
testGetItemSlice
self.failUnless(pySeq[1:] == d[1:])
IndexError: R object index out of range (highest index < lowest index)
----------------------------------------------------------------------
Ran 15 tests in 0.087s
FAILED (errors=1)
Testing: test_cleanup
.
----------------------------------------------------------------------
Ran 1 test in 1.619s
OK
impulsive$
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