I have an error that occurs only when I call lrtest (from the lmtest package) from a user-defined function via rpy2.
R:
continuous.test <- function(dat) {
require('lmtest')
options(warn=-1)
model <- lm(formula='pheno ~ .', data=dat)
anova <- lrtest(model,'interaction')
pval <- anova$"Pr(>Chisq)"[2]
}
When I call this function from the R interpreter, everything runs correctly. However, I receive an error when calling from the following snippet of python code. Note, this particular python file makes many other calls to rpy2 with success.
Python:
...
kway_dat = R.DataFrame(dataframe) # this is a valid dataframe, it's used in other calls.
...
R.r("source('/path/to/user/defined/file/perm_test.r')")
continuous_test = R.r['continuous.test']
pval = continuous_test(kway_dat)
Error:
Error in is.data.frame(data) : object 'dat' not found
Traceback (most recent call last):
File "./test_r_.py", line 83, in <module>
pval = continuous_test(kway_dat)
File "/usr/lib/python2.6/site-packages/rpy2-2.2.6dev_20120806-py2.6-linux-x86_64.egg/rpy2/robjects/functions.py", line 82, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/usr/lib/python2.6/site-packages/rpy2-2.2.6dev_20120806-py2.6-linux-x86_64.egg/rpy2/robjects/functions.py", line 34, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in is.data.frame(data) : object 'dat' not found
Troubleshooting:
I have tested the code in R and everything works fine.
I have passed a dataframe from python to R through rpy2 and called is.data.frame(dat) from an R function, and it returns true, so the issue is with lmtest or lrtest + rpy2.
Any help would be great. Thanks all!
It would be easier to help with a self-contained example (so one can reproduce exactly what you are experiencing).
A possible answer still: you might want to check that the content of the file
/path/to/user/defined/file/perm_test.r is really what you think it is.
I am also adding a stub for a self-contained example:
r_code = """
require('lmtest')
options(warn=-1)
continuous.test <- function(dat) {
model <- lm(formula='pheno ~ .', data=dat)
anova <- lmtest::lrtest(model,'interaction')
pval <- anova$"Pr(>Chisq)"[2]
}
"""
from rpy2.robjects import packages
my_r_pack = packages.SignatureTranslatedAnonymousPackage(r_code, "my_r_pack")
# [build a demo kway_dat here]
my_r_pack.continuous_test(kway_dat)
Answer Found
The issue was lrtest's internal call to update the model. Once inside lrtest, dat was out of scope. By updating the model manually and using lrtest's alternative call lrtest(model0,model1), the issue is entirely avoided.
Thanks to Achim Zeileis who replied incredibly promptly.
Related
i'm a newbie in python and coding,i'm trying to use pyzabbix to add trigger dependecies,but some error occusrs.
When i run
zapi.trigger.addDependencies(triggerid, dependsOnTriggerid)
an error occurs
pyzabbix.ZabbixAPIException: ('Error -32500: Application error., No permissions to referred object or it does not exist!', -32500)
i get the "triggerid" and "dependsOnTriggerid" by trigger.get:
triggerid_info = zapi.trigger.get(filter={'host': 'xx','description': 'xx'},output=['triggerid'], selectDependencies=['description'])
triggerid = triggerid_info[0]['triggerid']
dependsOnTriggerid = trigger_info[0]['dependencies'][0]['triggerid']
The results are as follws:
Traceback (most recent call last): File "E:/10.python/2019-03-07/1.py", line 14, in zapi.trigger.addDependencies(triggerid, dependsOnTriggerid) File "D:\Program Files\Python37\lib\site-packages\pyzabbix__init__.py", line 166, in fn args or kwargs File "D:\Program Files\Python37\lib\site-packages\pyzabbix__init__.py", line 143, in do_request raise ZabbixAPIException(msg, response_json['error']['code']) pyzabbix.ZabbixAPIException: ('Error -32500: Application error., No permissions to referred object or it does not exist!', -32500)
Did i get the wrong triggerid? or the i use the method in a wrong way? Thanks so much
To add a dependancy means that you need to link two different triggers (from the same host or from another one) with a master-dependent logic.
You are trying to add the dependancy triggerid -> dependsOnTriggerid, which is obtained from a supposed existing dependancy (trigger_info[0]['dependencies'][0]['triggerid']), and this makes little sense and I suppose it's the cause of the error.
You need to get both trigger's triggerid and then add the dependancy:
masterTriggerObj = zapi.trigger.get( /* filter to get your master trigger here */ )
dependentTriggerObj = zapi.trigger.get( /* filter to get your dependent trigger here */)
result = zapi.trigger.adddependencies(triggerid=dependentTriggerObj[0]['triggerid'], dependsOnTriggerid=masterTriggerObj[0]['triggerid'])
The method "trigger.addDependencies" need only one parameter，and it should be a dict or some other object/array.The following code solves the problem.
trigger_info = zapi.trigger.get(filter={xx},output=['triggerid'])
trigger_depends_info_193 = zapi.trigger.get(filter={xx},output=['triggerid'])
trigger_dependson_193 = {"triggerid": trigger_info[0]['triggerid'], "dependsOnTriggerid": trigger_depends_info_193[0]['triggerid']}
zapi.trigger.adddependencies(trigger_dependson_193)
Up until last week, I had a piece of code for calculating the odds of something occurring for a series of events, but starting this week the code doesn't work.
The code is the following:
import numpy as np
import pysal
import os
dbf = pysal.open('file.csv','r')
y = np.array([dbf.by_col('result')]).T
names_to_extract = ['dist', 'angle']
x = np.array([dbf.by_col(name) for name in names_to_extract]).T
id = np.array([dbf.by_col('incidenceId')]).T
model = pysal.spreg.probit.Probit(y, x, w=None, name_y='result', name_x=['dist','angle'], name_w=None, name_ds=None)
fin = np.column_stack((id, model.y, model.predy))
os.chdir("/destinyfolder")
np.savetxt('xg.csv', fin, delimiter=',', fmt='%d, %d, %f')
And I get this error:
/usr/local/lib/python3.7/site-packages/pysal/__init__.py:65: VisibleDeprecationWarning: PySAL's API will be changed on 2018-12-31. The last release made with this API is version 1.14.4. A preview of the next API version is provided in the `pysalnext` package. The API changes and a guide on how to change imports is provided at https://migrating.pysal.org
), VisibleDeprecationWarning)
Traceback (most recent call last):
File "xg.py", line 14, in <module>
model = pysal.spreg.probit.Probit(y, x, w=None, name_y='result', name_x=['dist','angle'], name_w=None, name_ds=None)
File "/usr/local/lib/python3.7/site-packages/pysal/spreg/probit.py", line 807, in __init__
n = USER.check_arrays(y, x)
File "/usr/local/lib/python3.7/site-packages/pysal/spreg/user_output.py", line 359, in check_arrays
if not spu.spisfinite(i):
File "/usr/local/lib/python3.7/site-packages/pysal/spreg/sputils.py", line 267, in spisfinite
return np.isfinite(a.sum())
File "/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py", line 36, in _sum
return umr_sum(a, axis, dtype, out, keepdims, initial)
TypeError: cannot perform reduce with flexible type
Usually, I only got the DeprecationWarning, but the code worked. Since today, the code doesn't work. Consider that I am currently using pysal 1.14.4, numpy 1.16.2 and scipy 1.2.1. I have not updated my code to pysal 2.0 because I couldn't figure out how to port this code to the new version (and that's why I got the DeprecationWarning in the first place).
Here's the file: file.csv
Can you help me to make this work?
Entries in your x are strings, convert them to float:
x = np.array(...).T.astype(np.float)
This will fail at first because of "NULL" values in file.csv, you need to either filter these out or specify what float value they should be converted to.
Before posting a question, try first a simple google search for an immediate answer. If you google this error along with "pysal 1.14.4", you will immediately find this solution:
TypeError: cannot perform reduce with flexible type
I'm using R to do some data manipulation. This is a part of a larger project that is mostly in Python, so I'm not using R directly but RPy2 instead. Things work fine until I get to the dplyr part.
This works:
from rpy2.robjects import r
Rcode = '''library(RODBC)
library(dplyr)
# ...
# a bunch of R code that fetches data from SQL Server
# ...'''.format(db_name = 'foo')
print r(Rcode)
That gives me the data I want.
But when I try to do some data manipulation with dplyr, like this:
from rpy2.robjects import r
Rcode = '''library(RODBC)
library(dplyr)
# ...
# a bunch of R code that fetches data from SQL Server
# ...
myData <- myData
%>% group_by(someDataField)'''.format(db_name = 'foo')
print r(Rcode)
I get an error:
Traceback (most recent call last):
File "myScript.py", line 53, in <module>
print r(Rcode)
File "C:\Python27\lib\site-packages\rpy2\robjects\__init__.py", line 268, in __call__
p = rinterface.parse(string)
ValueError: Error while parsing the string.
I've tried escaping the % signs, escaping the > sign, and putting them within quotation marks, but nothing worked.
What am I missing?
I've seen the other questions about the same error (like here and here) but they didn't help.
I'm using Python 2.7.10 and RPy2 2.5.6.
myData <- group_by(MyData,someDataField)
I'm running python2.5 and trying to use the astLib library to analyse WCS information in astronomical images. I try and get the object instanciated with the following skeleton code:
from astLib import astWCS
w = astWCS.WCS('file.fits') # error here
where file.fits is a string pointing to a valid fits file.
I have tried using the alternate method of passing a pyfits header object and this fails also:
import pyfits
from astLib import astWCS
f = pyfits.open('file.fits')
header = f[0].header
f.close()
w = astWCS.WCS(header, mode='pyfits') # error here also
The error is this:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/astro/phrfbf/build/lib/python2.6/site-packages/astLib/astWCS.py", line 79, in __init__
self.updateFromHeader()
File "/home/astro/phrfbf/build/lib/python2.6/site-packages/astLib/astWCS.py", line 119, in updateFromHeader
self.WCSStructure=wcs.wcsinit(cardstring)
File "/home/astro/phrfbf/build/lib/python2.6/site-packages/PyWCSTools/wcs.py", line 70, in wcsinit
return _wcs.wcsinit(*args)
TypeError: in method 'wcsinit', argument 1 of type 'char *'
When I run in ipython, I get the full error here on the pastebin
I know the astWCS module is a wrapped version of WCStools but i'd prefer to use the Python module as the rest of my code is in Python
Can anyone help with this problem?
Just found out the updated version of this library has fixed the problem, thanks for everyone's help
Oh sorry, I should have seen. Looking at the pastebin in more detail, the only error I can think of is that, for some reason the header has unicode in it. It can't be converted to char *, and you get the error. I tried searching for something in the header, but everything looks okay. Can you do this and post the output in another pastebin?
import pyfits
f = pyfits.open('file.fits')
header = f[0].header
f.close()
for x, i in enumerate(header.iteritems()):
if len(str(i[1])) >= 70:
print x, str(i[1])
cardlist = header.ascardlist()
cardstring = ""
for card in cardlist:
cardstring = cardstring + str(card)
print repr(cardstring)
Or, if you can check the header of your fits file for "funny" characters, getting rid of them should solve the issue.
I've recently been working on a Squish test script, and trying to do something like what's described in the solution at:
Total memory used by Python process?
The relevant snippets from my code are as follows:
def measureMemory():
w = wmi.WMI('.')
result = w.query("SELECT WorkingSet FROM Win32_PerfRawData_PerfProc_Process WHERE Name=\"some_program\"")
print result
for WorkingSet in result:
print WorkingSet
subset = result[0]
print subset['WorkingSet']
# return result[0]['WorkingSet']
for i in range(50):
memory = measureMemory()
if memory:
# test.passes("%d memory used during undo." % memory)
print memory
Unfortunately, I've run into an error whenever I actually try to run the thing, as can be seen below.
[<_wmi_object: \\USER-PC\root\cimv2:Win32_PerfRawData_PerfProc_Process.Name="some_program">]
instance of Win32_PerfRawData_PerfProc_Process
{
Name = "some_program";
WorkingSet = "19386368";
};
Traceback (most recent call last):
File "C:\Python26\Test scripts\Testify", line 25, in -toplevel-
memory = measureMemory()
File "C:\Python26\Test scripts\Testify", line 19, in measureMemory
print subset['WorkingSet']
File "C:\Python24\Lib\site-packages\win32com\client\dynamic.py", line 242, in __getitem__
raise TypeError("This object does not support enumeration")
TypeError: This object does not support enumeration
I'm not sure why this should be throwing an error, as I don't think I've changed anything significant from the example I took code from.
I'm using Python 2.4.4, if that's significant, and unfortunately I can't really upgrade, no matter how much it might help.
The WMI syntax seems to have changed from the examples. Try using subset.WorkingSet instead of subset['WorkingSet']