GREAT -- keep on the progressing forward!
My humble feedback:
$> python2.6 -m rpy2.tests; python2.6 -c 'import rpy2; print rpy2.__version__';
dpkg -l r-base-core
...F...Error in function (new = FALSE) : file choice cancelled
.................................................................................F......Loading
required package: splines
............Error in function (x) : object 'y' not found
....Error in .Primitive("sum")(c("a", "b", "c", "d", "e", "f", "g", "h", "i",
:
invalid 'type' (character) of argument
.................Error in function (description, open = "", blocking = FALSE,
encoding = getOption("encoding")) :
cannot open the connection
In addition: Warning message:
In function (description, open = "", blocking = FALSE, encoding =
getOption("encoding")) :
cannot create fifo '/home/yoh/.tmp/Rtmpne9cVP/Rf327b23c6', reason 'No such
file or directory'
E..............................Error in .Primitive("[")(0:10, list("a", "b",
"c")) :
invalid subscript type 'list'
..........................................................................................................
======================================================================
ERROR: testStr (rpy2.robjects.tests.testRObject.RObjectTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/robjects/tests/testRObject.py",
line 30, in testStr
s = prt.__str__()
File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/robjects/robject.py", line
29, in __str__
tmp = self.__fifo(rpy2.rinterface.StrSexpVector(["", ]))
RRuntimeError: Error in function (description, open = "", blocking = FALSE,
encoding = getOption("encoding")) :
cannot open the connection
======================================================================
FAIL: testInterruptR (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/rinterface/tests/test_EmbeddedR.py",
line 107, in testInterruptR
self.assertFalse(ret_code is None) # Interruption failed
AssertionError
======================================================================
FAIL: testNARealtoR (rpy2.rinterface.tests.test_SexpVector.NAValuesTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/yoh/proj/rpy2/build/lib.linux-x86_64-2.6/rpy2/rinterface/tests/test_SexpVector.py",
line 77, in testNARealtoR
self.assertEquals(True, ri.baseenv["is.na"](na_real)[0])
AssertionError: True != False
----------------------------------------------------------------------
Ran 265 tests in 1.498s
FAILED (failures=2, errors=1)
2.1.0beta2
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad)
||/ Name Version
Description
+++-=====================================-=====================================-==========================================================================================
ii r-base-core 2.10.1-2
GNU R core of statistical computation and graphics system
Another annoyance I've ran into today -- our pymvpa unittests keep segfaulting
in some non-R related places whenever rpy2 is in use. It was happening with
current version in sid: 2.1.0~20100314-1 and with current tip. Attached see
the valgrind output for python2.5 and version 2.1.0~20100314-1 (first
R issues seems to be not that critical -- happens also with 2.6 without
major problems).
(Un)fortunately this issue seems not to reveal (or being absent) with
python2.6 ... I wonder if there is anything I could help/do to figure
it out for 2.5 ;)
On Mon, 29 Mar 2010, Laurent Gautier wrote:
> Hi,
> rpy2-2.1beta3 is out and available on bitbucket and on sourceforge.
> This fixes bugs (such as a memory leak), plus adds last minute details.
> The next expected step is the release candidate, then the release.
> L.
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> rpy-list mailing list
> rpy-list@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rpy-list
--
.-.
=------------------------------ /v\ ----------------------------=
Keep in touch // \\ (yoh@|www.)onerussian.com
Yaroslav Halchenko /( )\ ICQ#: 60653192
Linux User ^^-^^ [175555]
==8438== Memcheck, a memory error detector
==8438== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
==8438== Using Valgrind-3.5.0-Debian and LibVEX; rerun with -h for copyright
info
==8438== Command: /usr/bin/python mvpa/tests/__init__.py
==8438==
T: MVPA_SEED=1
T: Testing for availability of external software packages.
WARNING: running ipython env is not available.
* Please note: warnings are printed only once, but underlying problem might
occur many times *
WARNING: lars is not available.
WARNING: nibabel is not available.
WARNING: shogun.svrlight is not available.
==8438== Conditional jump or move depends on uninitialised value(s)
==8438== at 0xBFE4290: inflateReset2 (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0xBFE437F: inflateInit2_ (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0xBFDDC86: ??? (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0x23190982: gzfile_open (connections.c:1169)
==8438== by 0x2318D467: do_gzfile (connections.c:1730)
==8438== by 0x23236D96: do_internal (names.c:1165)
==8438== by 0x231EF10B: Rf_eval (eval.c:464)
==8438== by 0x231F2AB9: Rf_applyClosure (eval.c:699)
==8438== by 0x231EEFF7: Rf_eval (eval.c:508)
==8438== by 0x231F10DF: do_set (eval.c:1502)
==8438== by 0x231EF10B: Rf_eval (eval.c:464)
==8438== by 0x231F11BB: do_begin (eval.c:1245)
==8438==
==8438== Conditional jump or move depends on uninitialised value(s)
==8438== at 0xBFE4290: inflateReset2 (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0xBFE437F: inflateInit2_ (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0xBFDEAD8: uncompress (in /usr/lib/libz.so.1.2.3.4)
==8438== by 0x23184E09: R_decompress1 (connections.c:5096)
==8438== by 0x232B134B: do_lazyLoadDBfetch (serialize.c:2343)
==8438== by 0x231EF23D: Rf_eval (eval.c:493)
==8438== by 0x231EF466: forcePromise (eval.c:331)
==8438== by 0x231EEE6B: Rf_eval (eval.c:445)
==8438== by 0x231D9642: Rf_findFun (envir.c:1293)
==8438== by 0x231EEF9E: Rf_eval (eval.c:451)
==8438== by 0x23222AD5: R_ReplFile (main.c:100)
==8438== by 0x23222BE9: R_LoadProfile (main.c:654)
==8438==
WARNING: good scipy.stats.rdist is not available.
WARNING: weave is not available.
WARNING: shogun.lightsvm is not available.
WARNING: pywt wp reconstruct fixed is not available.
test_externals (mvpa.tests.test_externals.TestExternals) ... ok
test_externals_correct2nd_invocation (mvpa.tests.test_externals.TestExternals)
... ok
test_externals_no_double_invocation (mvpa.tests.test_externals.TestExternals)
... ok
Very basic testing -- just to see if it doesn't crash ... ok
test_basic (mvpa.tests.test_dochelpers.DochelpersTests) ... ok
test_borrow_doc (mvpa.tests.test_dochelpers.DochelpersTests) ... ok
test_borrow_kwargs (mvpa.tests.test_dochelpers.DochelpersTests) ... ok
test_searchlight_doc (mvpa.tests.test_dochelpers.DochelpersTests) ... ok
test_simple_som (mvpa.tests.test_som.SOMMapperTests) ... ok
test_blank_state (mvpa.tests.test_state.StateTests) ... ok
test_deep_copying_state_variable (mvpa.tests.test_state.StateTests) ... ok
Check if we can store/restore set of enabled ca ... ok
test_parametrized (mvpa.tests.test_state.StateTests) ... ok
test_proper_state (mvpa.tests.test_state.StateTests) ... ok
Simple test if child gets conditional attributes from the parent as well ... ok
test_read_only (mvpa.tests.test_state.StateTests) ... ok
To test new ca ... ok
test_stored_temporarily (mvpa.tests.test_state.StateTests) ... ok
test_value_in_constructor (mvpa.tests.test_state.StateTests) ... ok
test_blank (mvpa.tests.test_params.ParamsTests) ... ok
test_classifier (mvpa.tests.test_params.ParamsTests) ... ok
test_mixed (mvpa.tests.test_params.ParamsTests) ... ok
test_simple (mvpa.tests.test_params.ParamsTests) ... ok
test_config (mvpa.tests.test_config.ConfigTests) ... ok
test_asobjarray (mvpa.tests.test_support.SupportFxTests) ... ok
test_break_points (mvpa.tests.test_support.SupportFxTests) ... ok
test_correlation (mvpa.tests.test_support.SupportFxTests) ... ok
test_event (mvpa.tests.test_support.SupportFxTests) ... ok
test_id_hash (mvpa.tests.test_support.SupportFxTests) ... ok
test_map_overlap (mvpa.tests.test_support.SupportFxTests) ... ok
test_mof_n_combinations (mvpa.tests.test_support.SupportFxTests) ... ok
Test our ad-hoc SmartVersion ... ok
test_transform_with_boxcar (mvpa.tests.test_support.SupportFxTests) ... ok
Test conversion of versions from strings ... ok
mvpa.tests.test_support.test_value2idx ... ok
Test if works fine with carriage return (cr) symbol ... ok
test_debug (mvpa.tests.test_verbosity.VerboseOutputTest) ... ok
test_debug_rgexp (mvpa.tests.test_verbosity.VerboseOutputTest) ... ok
Test error message ... ok
Test if it works fine with no newline (LF) symbol ... ok
Test once logger ... ok
Test if it doesn't output at higher levels ... ok
Test if outputs at lower levels and indents ... ok
Test indent symbol ... ok
Test if chokes on negative level ... ok
Test all available reports, real or dummy for just working ... ==8438== Invalid
read of size 1
==8438== at 0x4B6F98: ??? (in /usr/bin/python2.5)
==8438== by 0x446489: ??? (in /usr/bin/python2.5)
==8438== by 0x4B79E4: ??? (in /usr/bin/python2.5)
==8438== by 0x4B85D8: ??? (in /usr/bin/python2.5)
==8438== by 0x48DB17: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48EC8E: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48F4E0: PyEval_EvalCodeEx (in /usr/bin/python2.5)
==8438== by 0x48DEEF: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48EC8E: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48F4E0: PyEval_EvalCodeEx (in /usr/bin/python2.5)
==8438== by 0x4D6A7C: ??? (in /usr/bin/python2.5)
==8438== by 0x418492: PyObject_Call (in /usr/bin/python2.5)
==8438== Address 0xa9 is not stack'd, malloc'd or (recently) free'd
==8438==
==8438==
==8438== Process terminating with default action of signal 11 (SIGSEGV)
==8438== Access not within mapped region at address 0xA9
==8438== at 0x4B6F98: ??? (in /usr/bin/python2.5)
==8438== by 0x446489: ??? (in /usr/bin/python2.5)
==8438== by 0x4B79E4: ??? (in /usr/bin/python2.5)
==8438== by 0x4B85D8: ??? (in /usr/bin/python2.5)
==8438== by 0x48DB17: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48EC8E: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48F4E0: PyEval_EvalCodeEx (in /usr/bin/python2.5)
==8438== by 0x48DEEF: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48EC8E: PyEval_EvalFrameEx (in /usr/bin/python2.5)
==8438== by 0x48F4E0: PyEval_EvalCodeEx (in /usr/bin/python2.5)
==8438== by 0x4D6A7C: ??? (in /usr/bin/python2.5)
==8438== by 0x418492: PyObject_Call (in /usr/bin/python2.5)
==8438== If you believe this happened as a result of a stack
==8438== overflow in your program's main thread (unlikely but
==8438== possible), you can try to increase the size of the
==8438== main thread stack using the --main-stacksize= flag.
==8438== The main thread stack size used in this run was 8388608.
T: Tests from "test_lars" are skipped due to missing externals: ['lars',
'scipy']
T: Warning -- following test files were found but will not be tested:
test_lars.py
==8438==
==8438== HEAP SUMMARY:
==8438== in use at exit: 127,972,803 bytes in 89,405 blocks
==8438== total heap usage: 932,393 allocs, 842,988 frees, 918,422,040 bytes
allocated
==8438==
==8438== LEAK SUMMARY:
==8438== definitely lost: 3,586 bytes in 49 blocks
==8438== indirectly lost: 5,328 bytes in 171 blocks
==8438== possibly lost: 81,544,555 bytes in 61,848 blocks
==8438== still reachable: 46,419,334 bytes in 27,337 blocks
==8438== suppressed: 0 bytes in 0 blocks
==8438== Rerun with --leak-check=full to see details of leaked memory
==8438==
==8438== For counts of detected and suppressed errors, rerun with: -v
==8438== Use --track-origins=yes to see where uninitialised values come from
==8438== ERROR SUMMARY: 1941 errors from 3 contexts (suppressed: 47731 from 666)
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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