[codeface] AW: Re: AW: Re: AW: Re: AW: AW: Re: AW: Re: AW: Re: Unit tests - Exception in mailing list analysis executing batch.R
- From: Matthias Gemmer <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx>
- To: "codeface@xxxxxxxxxxxxx" <codeface@xxxxxxxxxxxxx>
- Date: Thu, 12 Feb 2015 19:03:51 +0000
>________________________________________
>Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im Auftrag
>von Matthias Dittrich <matthi.d@xxxxxxxxxxxxxx>
>Gesendet: Donnerstag, 12. Februar 2015 19:06
>An: codeface@xxxxxxxxxxxxx
>Betreff: [codeface] Re: AW: Re: AW: Re: AW: AW: Re: AW: Re: AW: Re: Unit tests
>- Exception in mailing list analysis executing batch.R
>Hi,
>On 12.02.2015 18:39, Matthias Gemmer wrote:
>>> ________________________________________
>>> Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im
>>> Auftrag von Mitchell Joblin <joblin.m@xxxxxxxxx>
>>> Gesendet: Freitag, 30. Januar 2015 23:28
>>> An: codeface@xxxxxxxxxxxxx
>>> Betreff: [codeface] Re: AW: Re: AW: AW: Re: AW: Re: AW: Re: Unit tests -
>>> Exception in mailing list analysis executing batch.R
>>> On Fri, Jan 30, 2015 at 11:03 PM, Matthias Gemmer
>>> <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx> wrote:
>>>> ________________________________
>>>>> [codeface] Re: AW: AW: Re: AW: Re: AW: Re: Unit tests - Exception in
>>>>> mailing list analysis executing batch.R
>>>>> codeface-bounce@xxxxxxxxxxxxx
>>>>> im Auftrag von
>>>>> Mitchell Joblin <joblin.m@xxxxxxxxx>
>>>>> Fr 30.01.2015 22:00
>>>>> An:
>>>>> codeface@xxxxxxxxxxxxx;
>>>>> On Jan 30, 2015 9:26 PM, "Matthias Gemmer"
>>>>> <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx> wrote:
>>>>>>
>>>>>> ________________________________
>>>>>> Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im
>>>>>> Auftrag von Matthias Gemmer <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx>
>>>>>> Gesendet: Freitag, 30. Januar 2015 20:35
>>>>>> An: codeface@xxxxxxxxxxxxx
>>>>>> Betreff: [codeface] AW: Re: AW: Re: AW: Re: Unit tests - Exception in
>>>>>> mailing list analysis executing batch.R
>>>>>>
>>>>>>
>>>>>> There is one error "left":
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ERROR: integration.test_exampleprojects
>>>>>> (unittest.loader.ModuleImportFailure)
>>>>>> ----------------------------------------------------------------------
>>>>>> ImportError: Failed to import test module:
>>>>>> integration.test_exampleprojects
>>>>>> Traceback (most recent call last):
>>>>>> File "/usr/lib/python2.7/unittest/loader.py", line 252, in _find_tests
>>>>>> module = self._get_module_from_name(name)
>>>>>> File "/usr/lib/python2.7/unittest/loader.py", line 230, in
>>>>>> _get_module_from_name
>>>>>> __import__(name)
>>>>>> File
>>>>>> "/home/matthias/codeface/codeface/test/integration/test_exampleprojects.py",
>>>>>> line 25, in <module>
>>>>>> from .example_projects import example_project_func
>>>>>> File
>>>>>> "/home/matthias/codeface/codeface/test/integration/example_projects.py",
>>>>>> line 17, in <module>
>>>>>> from .gitproject import GitProject
>>>>>> File "/home/matthias/codeface/codeface/test/integration/gitproject.py",
>>>>>> line 29
>>>>>> def __str__(self):
>>>>>> ^
>>>>>> IndentationError: expected an indented block
>>>>>>
>>>>>> ----------------------------------------------------------------------
>>>>>> Ran 3 tests in 0.086s
>>>>>>
>>>>>> FAILED (errors=1)
>>>>>>
>>>>>>
>>>>>> Sorry, the syntax error above was made on my side.
>>>>>>
>>>>>> Unit tests raise:
>>>>>>
>>>>>>
>>>>>> a) File "/home/matthias/codeface/codeface/cluster/cluster.py", line 1388,
>>>>>> in performAnalysis
>>>>>>
>>>>>> emitStatisticalData(cmtlist, id_mgr, logical_depends, outdir,
>>>>>> releaseRangeID,\
>>>>>> UnboundLocalError: local variable 'logical_depends' referenced before
>>>>>> assignment
>>>>>>
>>>>>> b) Exception: Command
>>>>>> '/home/matthias/codeface/codeface/R/cluster/persons.r --loglevel devinfo
>>>>>> --logfile /tmp/codeface_test_projectd3XgLf/.git/log.R.r0 -c
>>>>>> /home/matthias/codeface/codeface_testing.conf -p
>>>>>> /tmp/codeface_test_projectd3XgLfbYdrIG
>>>>>> /tmp/codeface_test_projectd3XgLf/.git/results/codeface_test_projectd3XgLf/proximity/v0_release-v1_release
>>>>>> 189' failed with exit code 1.
>>>>> I can't be certain but to me it looks like you are not running the latest
>>>>> code. Can you check that you fetched the latest and merged it to your
>>>>> local
>>>>> branch. Can you tell me the has of the latest commit you see on your
>>>>> branch?
>>>> The hash is 88db2d5.
>>> That's good, you are on the latest. Please edit the project
>>> configuration file (in the codeface/conf directory) by changing the
>>> "tagging" line to "proximity" or "feature" instead of "tag". Please
>>> let me know if those work. For example, the Linux conf file looks
>>> like:
>>> ==== Begin config file
>>> project: linux
>>> repo: linux # Relative to git-dir as specified on the command line
>>> description: Linux kernel
>>> mailinglists:
>>> - {name: gmane.linux.kernel, type: dev, source: gmane}
>>> revisions: ["v2.6.30", "v2.6.31", "v2.6.32", "v2.6.33", "v2.6.34",
>>>> "v2.6.35", "v2.6.36", "v2.6.37", "v2.6.38", "v2.6.39",
>>>> "v3.0", "v3.1", "v3.2", "v3.3", "v3.4", "v3.5", "v3.6",
>>>> "v3.7", "v3.8", "v3.9"]
>>> rcs: ["v2.6.30-rc1", "v2.6.31-rc1", "v2.6.32-rc1", "v2.6.33-rc1",
>>> "v2.6.34-rc1", "v2.6.35-rc1", "v2.6.36-rc1", "v2.6.37-rc1",
>>> "v2.6.38-rc1", "v2.6.39-rc1", "v3.0-rc1", "v3.1-rc1", "v3.2-rc1",
>>> "v3.3-rc1", "v3.4-rc1", "v3.5-rc1", "v3.6-rc1", "v3.7-rc1",
>>> "v3.8-rc1",
>>> "v3.9-rc1"]
>>> tagging: tag <=============================== Change here
>>> ======End config file
>>> Thanks,
>>> Mitchell
>> Sorry for the late reply.
>> Obviously I was not on the latest version. Now I surely have the one with
>> the hash 88db2d5.
>>
>> With "feature" and "tag" in the tagging-line of the config-file I get:
>You need at least 0144984d08d73ac14d41577f88fdfab33ecb2665 if you want
>to use the "tag" based analysis.
>>
>> $codeface run -c codeface.conf -p conf/linux-kernel.conf ../analysis/
>> ../projects/
>> ...
>> Pass 1/2: 100% |#################################################| Time:
>> 0:06:58
>> Traceback (most recent call last):
>> File "/home/matthias/.local/bin/codeface", line 9, in <module>
>> load_entry_point('codeface==0.2.0', 'console_scripts', 'codeface')()
>> File "/home/matthias/codeface/codeface/cli.py", line 198, in main
>> return run(sys.argv)
>> File "/home/matthias/codeface/codeface/cli.py", line 194, in run
>> return args.func(args)
>> File "/home/matthias/codeface/codeface/cli.py", line 112, in cmd_run
>> args.profile_r, args.jobs, args.tagging)
>> File "/home/matthias/codeface/codeface/project.py", line 110, in
>> project_analyse
>> endmsg=prefix + "Commit analysis done."
>> File "/home/matthias/codeface/codeface/util.py", line 109, in add
>> func(*args, **kwargs)
>> File "/home/matthias/codeface/codeface/cluster/cluster.py", line 1900, in
>> doProjectAnalysis
>> rc_range)
>> File "/home/matthias/codeface/codeface/cluster/cluster.py", line 1806, in
>> performAnalysis
>> populatePersonDB(cmtdict.values(), id_mgr, link_type)
>> File "/home/matthias/codeface/codeface/cluster/cluster.py", line 1357, in
>> populatePersonDB
>> ID = id_mgr.getPersonID(cmt.get
>> AuthorName())
>> File "/home/matthias/codeface/codeface/cluster/idManager.py", line 141, in
>> getPersonID
>> self._cache[(name, email)] = self._query_user_id(name, email)
>> File "/home/matthias/codeface/codeface/cluster/idManager.py", line 123, in
>> _query_user_id
>> jsond = json.loads(result)
>> File "/usr/lib/python2.7/json/__init__.py", line 326, in loads
>> return _default_decoder.decode(s)
>> File "/usr/lib/python2.7/json/decoder.py", line 365, in decode
>> obj, end = self.raw_decode(s, idx=_w(s, 0).end())
>> File "/usr/lib/python2.7/json/decoder.py", line 383, in raw_decode
>> raise ValueError("No JSON object could be decoded")
>> ValueError: No JSON object could be decoded
>> ----------------------------
>To me that looks like the id_service is not running, something else is
>running on its port (8080) or something is blocking the connection
>(firewall?).
>>
>> When I set "proximity" as tagging, there is repeatedly the warning:
>> ignoring unsupported tag ...
>> Finally a memory error appears.
>I thing I had similar problems before and just used 4gb a swap file (8gb
>total). No more problems since then. How much memory is available on
>your system?
Thanks for your fast answer, Mitchell.
$ free -m
total used free shared buffers cached
Mem: 3965 1853 2111 0 117 950
-/+ buffers/cache: 786 3179
Swap: 0 0 0
The size of a page is 4MB.
What can/shall I do?
>Hope this helps,
> Matthias
>>
>> Best regards,
>> Matthias
>>>>
>>>>> Thanks,
>>>>> Mitchell
>>>>>> -- Matthias
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im
>>>>>> Auftrag von Mitchell Joblin <joblin.m@xxxxxxxxx>
>>>>>> Gesendet: Freitag, 30. Januar 2015 20:33
>>>>>> An: codeface@xxxxxxxxxxxxx
>>>>>> Betreff: [codeface] Re: AW: Re: AW: Re: Unit tests - Exception in mailing
>>>>>> list analysis executing batch.R
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 30, 2015 8:22 PM, "Matthias Gemmer"
>>>>>> <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx> wrote:
>>>>>>> I ran the analysis (with the updated code) for jquery and qemu. In both
>>>>>>> cases I got:
>>>>>> Can you run the tests without error now?
>>>>>>
>>>>>> --Mitchell
>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>> File "/home/matthias/.local/bin/codeface", line 9, in <module>
>>>>>>> load_entry_point('codeface==0.2.0', 'console_scripts',
>>>>>>> 'codeface')()
>>>>>>> File "/home/matthias/codeface/codeface/cli.py", line 191, in main
>>>>>>> return run(sys.argv)
>>>>>>> File "/home/matthias/codeface/codeface/cli.py", line 187, in run
>>>>>>> return args.func(args)
>>>>>>> File "/home/matthias/codeface/codeface/cli.py", line 106, in cmd_run
>>>>>>> args.profile_r, args.jobs)
>>>>>>> File "/home/matthias/codeface/codeface/project.py", line 93, in
>>>>>>> project_analyse
>>>>>>> endmsg=prefix + "Commit analysis done."
>>>>>>> File "/home/matthias/codeface/codeface/util.py", line 104, in add
>>>>>>> func(*args, **kwargs)
>>>>>>> File "/home/matthias/codeface/codeface/cluster/cluster.py", line
>>>>>>> 1418, in doProjectAnalysis
>>>>>>> rc_range)
>>>>>>> File "/home/matthias/codeface/codeface/cluster/cluster.py", line
>>>>>>> 1388, in performAnalysis
>>>>>>> emitStatisticalData(cmtlist, id_mgr, logical_depends, outdir,
>>>>>>> releaseRangeID,\
>>>>>>> UnboundLocalError: local variable 'logical_depends' referenced before
>>>>>>> assignment
>>>>>>> ________________________________________
>>>>>>> Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im
>>>>>>> Auftrag von Mitchell Joblin <joblin.m@xxxxxxxxx>
>>>>>>> Gesendet: Freitag, 30. Januar 2015 16:34
>>>>>>> An: codeface@xxxxxxxxxxxxx
>>>>>>> Betreff: [codeface] Re: AW: Re: Unit tests - Exception in mailing list
>>>>>>> analysis executing batch.R
>>>>>>>
>>>>>>> Hi Matthias,
>>>>>>>
>>>>>>> On Fri, Jan 30, 2015 at 3:08 PM, Matthias Gemmer
>>>>>>> <matthias.gemmer@xxxxxxxxxxxxxxxxxxxx> wrote:
>>>>>>>> I cloned the latest commit of the branch "mitchell-updates" and
>>>>>>>> installed codeface.
>>>>>>>> There are the following failures running unit tests:
>>>>>>> The test suite is broken in the version you pulled, I just merged some
>>>>>>> new code that disables the broken tests. Some tests broke because of
>>>>>>> changes to R dependencies. Despite the failing tests, the analysis
>>>>>>> will perform correctly. The tests need to be updated to account for
>>>>>>> the interface changes and this will happen soon. Please give the
>>>>>>> latest code a try and let me know if you experience any other issues.
>>>>>>>
>>>>>>> If you are going to run code on the mitchell-updates branch then you
>>>>>>> also need to install doxygen. Sorry that wasn't mentioned in the
>>>>>>> installation guide, once it's merged to master I will change that.
>>>>>>>
>>>>>>> Kind regards,
>>>>>>>
>>>>>>> Mitchell
>>>>>>>
>>>>>>>> 1) IOError: [Errno 2] No such file or directory:
>>>>>>>> '/tmp/does_not_exist_42_42'
>>>>>>>> 2015-01-30 15:57:19 [codeface.configuration] MainProcess ERROR:
>>>>>>>> Could not parse configuration file '/tmp/tmp4cq_OI'
>>>>>>>>
>>>>>>>> 2) [codeface.util] MainProcess ERROR: Command 'Rscript -e
>>>>>>>> library(testthat); if (test_dir(".")$n > 0) stop("Some tests failed.")'
>>>>>>>> failed with exit code 1.
>>>>>>>>
>>>>>>>> 3) [codeface.configuration] MainProcess CRITICAL: Malformed
>>>>>>>> configuration: revision and rcs list lengths differ! Found 5 revisions
>>>>>>>> and 4
>>>>>>>> release candidates.
>>>>>>>>
>>>>>>>> 4) [codeface.VCS] MainProcess CRITICAL: doxygen analysis error[Errno
>>>>>>>> 2] No such file or directory - defaulting to Ctags
>>>>>>>>
>>>>>>>> 5) [codeface.util] MainProcess ERROR: Command
>>>>>>>> '/home/matthias/codeface/codeface/R/cluster/persons.r --loglevel
>>>>>>>> devinfo
>>>>>>>> --logfile /tmp/codeface_test_project9FdvGm/.git/log.R.r0 -c
>>>>>>>> /home/matthias/codeface/codeface_testing.conf -p
>>>>>>>> /tmp/codeface_test_project9FdvGm3NuXGh
>>>>>>>> /tmp/codeface_test_project9FdvGm/.git/results/codeface_test_project9FdvGm/proximity/v0_release-v1_release
>>>>>>>> 153' failed with exit code 1.
>>>>>>>>
>>>>>>>> Best Regards,
>>>>>>>> Matthias Gemmer
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> Von: codeface-bounce@xxxxxxxxxxxxx <codeface-bounce@xxxxxxxxxxxxx> im
>>>>>>>> Auftrag von Wolfgang Mauerer <wm@xxxxxxxxxxxxxxxx>
>>>>>>>> Gesendet: Dienstag, 27. Januar 2015 13:16
>>>>>>>> An: codeface@xxxxxxxxxxxxx
>>>>>>>> Betreff: [codeface] Re: Unit tests - Exception in mailing list
>>>>>>>> analysis executing batch.R
>>>>>>>>
>>>>>>>> Am 27/01/2015 12:55, schrieb Mitchell Joblin:
>>>>>>>>> On Tue, Jan 27, 2015 at 9:03 AM, Wolfgang Mauerer
>>>>>>>>> <wm@xxxxxxxxxxxxxxxx> wrote:
>>>>>>>>>>
>>>>>>>>>> Am 26/01/2015 17:33, schrieb Matthias Gemmer:
>>>>>>>>>>> Hello,
>>>>>>>>>>>
>>>>>>>>>>> I am using R version 3.1.2. All required packages should be
>>>>>>>>>>> installed
>>>>>>>>>>> correctly.
>>>>>>>>>>>
>>>>>>>>>>> Running the unit tests still raises an exception, something goes
>>>>>>>>>>> wrong
>>>>>>>>>>> in the mailinglist analysis:
>>>>>>>>>>>
>>>>>>>>>>> Exception: Command '/home/matthias/codeface/codeface/R/ml/batch.r
>>>>>>>>>>> --logfile /tmp/codeface_test_projectH8ZL0F/.git/log.R.ml.0
>>>>>>>>>>> --loglevel
>>>>>>>>>>> devinfo -c /home/matthias/codeface/codeface_testing.conf -p
>>>>>>>>>>> /tmp/codeface_test_projectH8ZL0F/.git/testproject.conf -j 1
>>>>>>>>>>>
>>>>>>>>>>> /tmp/codeface_test_projectH8ZL0F/.git/results/codeface_test_projectH8ZL0F/ml
>>>>>>>>>>> /tmp/codeface_test_projectH8ZL0F/.git
>>>>>>>>>>> codeface_test_projectH8ZL0F.dev1'
>>>>>>>>>>> failed with exit code 1.
>>>>>>>>>>>
>>>>>>>>>>> The log file says:
>>>>>>>>>>> $cat /tmp/codeface_test_projectH8ZL0F/.git/log.R.ml.0
>>>>>>>>>>> ...
>>>>>>>>>>> 2015-01-26 14:49:40 [codeface.R.ml.analysis] INFO: Starting
>>>>>>>>>>> mailinglist
>>>>>>>>>>> analysis
>>>>>>>>>>> 2015-01-26 14:49:40 [codeface.R] INFO: Traceback:
>>>>>>>>>>> 0:
>>>>>>>>>>> 1: config.script.run({
>>>>>>>>>>> positional.args <- list("resdir", "mldir", "listname
>>>>>>>>>>> 2: withCallingHandlers(expr, error = function(e) {
>>>>>>>>>>> if (!interactive()) {
>>>>>>>>>>>
>>>>>>>>>>> 3: dispatch.all(conf, conf$mldir, conf$resdir)
>>>>>>>>>>> 4: gen.forest(conf, repo.path, resdir)
>>>>>>>>>>> 5: gen.corpus(conf$listname, repo.path, suffix = ".mbox", marks
>>>>>>>>>>> =
>>>>>>>>>>> c("^_{10,}",
>>>>>>>>>>> 6: preprocess(corp)
>>>>>>>>>>> 7: sapply(corp, Author)
>>>>>>>>>>> 8: match.fun(FUN)
>>>>>>>>>>> 2015-01-26 14:49:40 [codeface.R] CRITICAL: object 'Author' not
>>>>>>>>>>> found
>>>>>>>>>> package tm changed the interface in the latest release (0.6) and
>>>>>>>>>> does
>>>>>>>>>> not pro function Author() any more. The replacement call is meta(),
>>>>>>>>>> see
>>>>>>>>>> http://cran.r-project.org/web/packages/tm/tm.pdf.
>>>>>>>>>> The call to Author() needs to be changed (or a replacement provided
>>>>>>>>>> via meta()); can you please file an appropriate bug? Or better
>>>>>>>>>> still, submit a patch :)
>>>>>>>>> No need to send a patch for this. I fixed this a while back in
>>>>>>>>> eef75f98 on the mitchell-updates branch, it just hasn't been merged
>>>>>>>>> to
>>>>>>>>> master yet. Now that I can commit to master I will merge that very
>>>>>>>>> soon.
>>>>>>>> great, I did not realise that. I agree that it's high time we merge
>>>>>>>> your updates branch. I'm fine with the branch.
>>>>>>>>
>>>>>>>> Cheers, Wolfgang
>>>>>>>>> --Mitchell
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thanks & best regards, Wolfgang Mauerer
>>>>>>>>>>
>>>>>>>>>>> 2015-01-26 14:49:40 [codeface.R] INFO: Error dump was written to
>>>>>>>>>>> 'error.dump.rda'.
>>>>>>>>>>> 2015-01-26 14:49:40 [codeface.R] INFO: To debug, launch R and run
>>>>>>>>>>> 'load("error.dump.rda"); debugger(error.dump)'
>>>>>>>>>>>
>>>>>>>>>>> Attached you can find the error dump.
>>>>>>>>>>>
>>>>>>>>>>> Kind regards,
>>>>>>>>>>> Matthias
Other related posts:
