biolab / orange2 Goto Github PK

Hi,

Can anyone help with the error below when I call the code?

import Orange
iris = Orange.data.Table("iris.tab")
pca = Orange.projection.linear.Pca(iris)
transformed_data = pca(iris)

ERROR:
import Orange
iris = Orange.data.Table("iris.tab")
pca = Orange.projection.pca(iris)
transformed_data = pca(iris)
Traceback (most recent call last):
File "", line 4, in
pca = Orange.projection.pca(iris)
TypeError: 'module' object is not callable

Installing Orange on an Ubuntu machine is a big hassle. Have you considered releasing Orange on a ppa repository?

I have a single column csv that looks like this:

6133569
6139630
6144413
6145451
6148248
6953464
7396414
7405092
10083050

and I want to import it into orange just to make a histogram out of it... but when I open it using the file datasource, I get the following error:

--------------------------------------------------------------------------------
Error                                         Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/Data/OWFile.py", line 797, in browse
    params=loader_for_path(path).params)
  File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/Data/OWFile.py", line 1005, in loader_for_path
    dialect, has_header = sniff_csv(path)
  File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/Data/OWFile.py", line 1024, in sniff_csv
    dialect = snifer.sniff(sample)
  File "/usr/lib/python2.7/csv.py", line 188, in sniff
    raise Error, "Could not determine delimiter"
Error: Could not determine delimiter

I'm running Orange 2.7.8.dev-2576588

@kernc I use a build-in installer in Anaconda, when I finish it and run I always get the jupyter's homepage. I really want to use the Anaconda but it have version mismatch (py2.7.12 64 bit & py2.7.6 32 bit ). So is it possible to run Orange in my Anaconda or I should use Anaconda with py3? Any success example using it ? #41

Running:

pip install --global-option="build_pyqt_ext" orange

(where pip belongs to a local user anaconda distribution)
I get the following:

Collecting orange
  Downloading Orange-2.7.8.tar.gz (15.0MB)
    100% |################################| 15.0MB 25kB/s 
Requirement already satisfied (use --upgrade to upgrade): setuptools in ./anaconda/lib/python2.7/site-packages/setuptools-14.0-py2.7.egg (from orange)
Requirement already satisfied (use --upgrade to upgrade): numpy in ./anaconda/lib/python2.7/site-packages (from orange)
Requirement already satisfied (use --upgrade to upgrade): scipy in ./anaconda/lib/python2.7/site-packages (from orange)
Installing collected packages: orange
  Running setup.py install for orange
    moc -o build/temp.linux-x86_64-2.7/point.moc source/orangeqt/point.h
    moc -o build/temp.linux-x86_64-2.7/multicurve.moc source/orangeqt/multicurve.h
    source/orangeqt/multicurve.h:0: Note: No relevant classes found. No output generated.
    moc -o build/temp.linux-x86_64-2.7/curve.moc source/orangeqt/curve.h
    moc -o build/temp.linux-x86_64-2.7/plot.moc source/orangeqt/plot.h
    moc -o build/temp.linux-x86_64-2.7/networkcurve.moc source/orangeqt/networkcurve.h
    source/orangeqt/networkcurve.h:0: Note: No relevant classes found. No output generated.
    moc -o build/temp.linux-x86_64-2.7/unconnectedlinescurve.moc source/orangeqt/unconnectedlinescurve.h
    moc -o build/temp.linux-x86_64-2.7/plotitem.moc source/orangeqt/plotitem.h
    building 'Orange.orangeqt' extension
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-cxRjYV/orange/setup.py", line 876, in <module>
        setup_package()
      File "/tmp/pip-build-cxRjYV/orange/setup.py", line 872, in setup_package
        ext_modules = ext_modules,
      File "/home/jack/anaconda/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/home/jack/anaconda/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/home/jack/anaconda/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 337, in run
        self.build_extensions()
      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 446, in build_extensions
        self.build_extension(ext)
      File "/tmp/pip-build-cxRjYV/orange/source/orangeqt/setup.py", line 228, in build_extension
        sipdistutils.build_ext.build_extension(self, ext)
      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 111, in build_extension
        build_ext_base.build_extension(self, ext)
      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 468, in build_extension
        sources = self.swig_sources(sources, ext)
      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 155, in swig_sources
        self._sip_compile(sip_bin, sip, sbf)
      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 166, in _sip_compile
        "-I", self._sip_sipfiles_dir(),
      File "/tmp/pip-build-cxRjYV/orange/source/orangeqt/setup.py", line 256, in _sip_sipfiles_dir
        if os.path.isdir(pyqt_sip_dir):
      File "/home/jack/anaconda/lib/python2.7/genericpath.py", line 41, in isdir
        st = os.stat(s)
    TypeError: coercing to Unicode: need string or buffer, NoneType found
    Complete output from command /home/jack/anaconda/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-cxRjYV/orange/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" build_pyqt_ext install --record /tmp/pip-60mW8g-record/install-record.txt --single-version-externally-managed --compile:
    running build_pyqt_ext

    creating build

    creating build/temp.linux-x86_64-2.7

    moc -o build/temp.linux-x86_64-2.7/point.moc source/orangeqt/point.h

    moc -o build/temp.linux-x86_64-2.7/multicurve.moc source/orangeqt/multicurve.h

    source/orangeqt/multicurve.h:0: Note: No relevant classes found. No output generated.

    moc -o build/temp.linux-x86_64-2.7/curve.moc source/orangeqt/curve.h

    moc -o build/temp.linux-x86_64-2.7/plot.moc source/orangeqt/plot.h

    moc -o build/temp.linux-x86_64-2.7/networkcurve.moc source/orangeqt/networkcurve.h

    source/orangeqt/networkcurve.h:0: Note: No relevant classes found. No output generated.

    moc -o build/temp.linux-x86_64-2.7/unconnectedlinescurve.moc source/orangeqt/unconnectedlinescurve.h

    moc -o build/temp.linux-x86_64-2.7/plotitem.moc source/orangeqt/plotitem.h

    building 'Orange.orangeqt' extension

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

      File "/tmp/pip-build-cxRjYV/orange/setup.py", line 876, in <module>

        setup_package()

      File "/tmp/pip-build-cxRjYV/orange/setup.py", line 872, in setup_package

        ext_modules = ext_modules,

      File "/home/jack/anaconda/lib/python2.7/distutils/core.py", line 151, in setup

        dist.run_commands()

      File "/home/jack/anaconda/lib/python2.7/distutils/dist.py", line 953, in run_commands

        self.run_command(cmd)

      File "/home/jack/anaconda/lib/python2.7/distutils/dist.py", line 972, in run_command

        cmd_obj.run()

      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 337, in run

        self.build_extensions()

      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 446, in build_extensions

        self.build_extension(ext)

      File "/tmp/pip-build-cxRjYV/orange/source/orangeqt/setup.py", line 228, in build_extension

        sipdistutils.build_ext.build_extension(self, ext)

      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 111, in build_extension

        build_ext_base.build_extension(self, ext)

      File "/home/jack/anaconda/lib/python2.7/distutils/command/build_ext.py", line 468, in build_extension

        sources = self.swig_sources(sources, ext)

      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 155, in swig_sources

        self._sip_compile(sip_bin, sip, sbf)

      File "/home/jack/anaconda/lib/python2.7/site-packages/sipdistutils.py", line 166, in _sip_compile

        "-I", self._sip_sipfiles_dir(),

      File "/tmp/pip-build-cxRjYV/orange/source/orangeqt/setup.py", line 256, in _sip_sipfiles_dir

        if os.path.isdir(pyqt_sip_dir):

      File "/home/jack/anaconda/lib/python2.7/genericpath.py", line 41, in isdir

        st = os.stat(s)

    TypeError: coercing to Unicode: need string or buffer, NoneType found

    ----------------------------------------
    Command "/home/jack/anaconda/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-cxRjYV/orange/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" build_pyqt_ext install --record /tmp/pip-60mW8g-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-cxRjYV/orange

I am dealing with continuous features and discrete class_var, i.e.

atts = ['a','b','c','d']
domain = Orange.data.Domain([Orange.feature.Continuous(x) for x in atts[:-1]] +
                            [Orange.feature.Discrete(atts[-1])])
data = Orange.data.Table(domain)
data.append([1,2,3,0])

However, it said "value index 0 out of range (0 - -1) at attribute no 4 (d)". Please help!

When installing Orange 3.3.7, I noticed the directory Orange/widgets/_highcharts/. The Highcharts JavaScript charting library is licensed under the CreativeCommons - Non Commercial 3.0 license, and may not be compatible with the Orange licenses, such as GNU GPL, or Free Software/Open Source licenses in general.

Proposed solution

Deprecate the Highcharts library in favor of a JavaScript charting library with free/open source compatible licensing terms. E.g.

• NVD3
• Plotly.js
• Vega

References

Highcharts license

Highcharts is available under various licenses depending on the intended usage. This conflicts with both the Free Software and Open Source definitions.

Free Software definition

• The freedom to run the program as you wish, for any purpose (freedom 0).

Open Source definition

• 6. No Discrimination Against Fields of Endeavor

The license must not restrict anyone from making use of the program in a specific field of endeavor. For example, it may not restrict the program from being used in a business, or from being used for genetic research.

Annotated Open Source Definition

Creative Commons and GPL / other open source

At best, the following Creative Commons licenses are compatible with Copyleft / open-source licenses:

• CC Zero
• CC - by
• CC - by- SA

On October 8, 2015 Creative Commons concluded that the CC BY-SA 4.0 is one-way compatible with the GPLv3.

Wikipedia: License compatibility

Creative Commons license compatibility matrix

Hi All
Orange is a great package,the GUI is great, the functionality is great and has been a fantastic resource to help some of our students overcome their fear to Machine Learning and computer/data science!

I was wondering if you could point me to some "How To's" or tutorials/resources for building a similar kind of GUI.

We are working with Docker and looking to build some easy pipelines for common bioinformatic workflows - focusing on NGS analysis first, and I think the structure off the Ornage GUI would be a great backbone to build upon.

I'm new the GUI building world, and only just dipping my toe in the Python world (dont hate me)...

Cheers

Steve & Team

When initially running the app, bad link in the get started button

In some of the visualization modules--I've tested parallel coordinate plots, Radviz, and survey plots--data labels on points or on the axes are being cropped oddly by the display window. For parallel coordinate plots and Radviz, this extends to those labels being cropped even in the report or saved pngs. On Radviz, the weird cropping behavior extends to data labels even when zoomed in.

I've attached images of the behavior. I'm running the Orange Snapshot bundle, build 2.7.8, under OS X Mavericks (10.9.5).

Parallel Coordinate Plot of cars-mpg data -- The y axis is mostly invisible, off to the left.
Radviz of Breast Cancer Data -- Two data labels are cropped by the edges of the plot area
Zoomed Radviz -- The data label "displacement" continues to be cropped by the edge of the plot area, no matter how zoomed in
Edit, 4/12/15: The clipping problem with data labels on RadViz does not happen with continuous variables, provided a legend is attached to the plot. Radviz of cars-mpg using a continuous variable doesn't have the cropping problem.

Hi everyone!
I have some perplexing questions while using Orange(version 3.11). I sampled a subset from the input dataset by Data Sampler widget to train a Logistic Regression , parameters like this:

Sampling type: Random sample with 70 % of data, stratified (if possible), deterministic
Input: 178 instances
Sample: 125 instances
Remaining: 53 instances

then I used the Test&Score widget to see the result by setting "Stratified 10-fold Cross validation" and I got the result like this:

Method AUC CA F1 Precision Recall
Logistic Regression 0.751 0.776 0.757 0.756 0.776

the test result on testdata like this:

Method AUC CA F1 Precision Recall
Logistic Regression 0.709 0.736 0.709 0.704 0.736

After that, I extracted the trainning data and test data which sampled by the Data Sampler widget with a python program, and used the trainning data to train a Logistic Regression model(parameter is the same like previous) , used the test data to validate the model, but I got the different result both in trainning and testing(all the parameters are the same), why?
Another question is how to output the detail parameters when sampling (i.e. the random seed and the test data), is it feasible?
Maybe these questions are quite stupid, I hope to get your help, thanks!

Hello,

I've attempted to install Orange (Win7, 64 bit), but it will not open. I have Python 2.7 as well as Python 3.4 installed (3.4 installed with Orange). Nothing happens when attempting to open the program. I've rebooted as well. I see Orange in C:\Python34\Lib\site-packages\Orange. Any help is appreciated.

Thanks.

No problems with plotting scree plot for PCA.

However the biplot for the top two components is not showing.

The documentation for PCA biplot says "components (list) – List of two components to plot." I have tried [0,1] to no avail either. Am I misunderstanding something?

That was an exageration.

But for 10,000 test samples it takes like 30mins- 1 hour, which doesn't make sense. All its doing is running a sample by the NN.

Please explain to me why this should take all day.

Thanks.

I am right now using Python2.7 and tried to install Orange2.7.8 but some problems occurred. Can someone figure out what is going on? Thank you!

After I did
$ python setup.py build
$ python setup.py install

And then ran:
$ orange-canvas

It showed:

Traceback (most recent call last):
File "/usr/local/bin/orange-canvas", line 9, in
load_entry_point('Orange==2.7.8', 'gui_scripts', 'orange-canvas')()
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 542, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2569, in load_entry_point
return ep.load()
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2229, in load
return self.resolve()
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 2235, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeCanvas/main.py", line 18, in
from PyQt4.QtGui import QFont, QColor

Hello, everyone:
when I come to deal with the problem that an instance is related with 2 or more labels, what should I do? deadly hope that someone can help me, Thanks a lot!!!

For any dataset even for the given ones, the File widget reports this error.

I tried my csv file and adult.tab and car.tab datasets. Result is always same

UnicodeDecodeError Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/OWWidget.py", line 179, in reportAndFinish
self.finishReport()
File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/OWWidget.py", line 298, in finishReport
sender=self)
File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/OWReport.py", line 186, in appendReport
self.addEntry(widnode)
File "/usr/local/lib/python2.7/dist-packages/Orange/OrangeWidgets/OWReport.py", line 198, in addEntry
widnode.time, widnode.data)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc5 in position 2: ordinal not in range(128)

Sorry for the stupid question, but is there a way to create a basket like this

Bread, Milk
Bread, Diapers, Beer, Eggs
Milk, Diapers, Beer, Cola
Bread, Milk, Diapers, Beer
Bread, Milk, Diapers, Cola

without using .basket files?

I also asked it on stackoverflow.

After installing Orange 3.3.7 on Ubuntu 16.04, the user interface icons and buttons fail to render correctly.

Environment

• Ubuntu 16.04
• Orange 3.3.7
• Anaconda 3.x
• Python 3.5

Hi,

I made a standalone app that writes a folder of .tab files to a database. It uses char(N) for categorical variables and text for meta strings (Orange).

Anyway, upon reading the table back in using SQL Reader that comes with Orange, all my classes are string metas.

Maybe they were accidentally written in as text. I will check that.

Thanks.

Obtained a Brier score greater than 1 when running 5 folds cross validation using Naive Bayes. Wikipedia claims the range of Brier scores to be between 0 and 1. Can someone verify if this was an error? Thanks.

MOVED TO Orange3 repository as suggested. LINK:
biolab/orange3#2607

I have downloaded the last Orange3 version for Mac (Orange3-3.5.0.dmg), installed it as described and tried to open it using right click, open.

The orange icon appears briefly and then disappears. No GUI is loaded. I managed to keep the Orange3 icon on the dock but no matter what I do to open it it always automatically close without providing any system error.

I did not have any version of Python installed on this system (which was the issue I read here for another user with Windows 7).

Hi Orange Dev Team - any plans to include functionality for readlng and loading RData files/objects?
Running the following version of Orange:-

I cloned the git repository, then followed installation instructions. I installed dependencies "on the road" until the orange-canvas successfully started.
But on the Data widgets list I find only Quick Select. When clicking on Help -> About Orange
I've an Output Windows containing the following:

There were problems importing the following widgets:
   OWRScript: No module named rpy2.robjects
   OWCorrelations: No module named Qwt5
   OWTimeDataVisualizer: No module named Qwt5
   OWPerformanceCurves: No module named Qwt5
   OWCalibratedClassifier: No module named Qwt5
   OWC45Tree: c45 is not found
   OWLiftCurve: No module named Qwt5
   OWCalibrationPlot: No module named Qwt5
   OWROC: No module named Qwt5
   OWParallelCoordinates: No module named Qwt5.Qwt
   OWLinProj: No module named Qwt5
   OWCorrespondenceAnalysis: No module named Qwt5
   OWSurveyPlot: No module named Qwt5
   OWScatterPlot: No module named Qwt5
   OWMultiCorrespondenceAnalysis: No module named Qwt5
   OWDistributions: No module named Qwt5
   OWSieveMultigram: No module named Qwt5
   OWRadviz: No module named Qwt5
   OWPolyviz: No module named Qwt5
   OWLinProj3D: cannot import name orangeqt
   OWScatterPlotQt: cannot import name orangeqt
   OWParallelCoordinatesQt: cannot import name orangeqt
   OWNxExplorer3D: No module named OWNxExplorerQt
   OWSphereviz3D: cannot import name orangeqt
   OWScatterPlot3D: cannot import name orangeqt
   OWMDSQt: cannot import name orangeqt
   OWRadvizQt: cannot import name orangeqt
   OWDistributionsQt: cannot import name orangeqt
   OWPolyvizQt: cannot import name orangeqt
   OWDiscretizeQt: cannot import name orangeqt
   OWLinProjQt: cannot import name orangeqt
   OWPCA: No module named Qwt5
   OWMDS: No module named Qwt5
The following widgets could not be imported and will not be available: OWSphereviz3D, OWLiftCurve, OWC45Tree, OWSurveyPlot, OWLinProjQt, OWScatterPlotQt, OWParallelCoordinatesQt, OWPCA, OWLinProj, OWMDSQt, OWDistributions, OWDiscretizeQt, OWMultiCorrespondenceAnalysis, OWScatterPlot, OWLinProj3D, OWMDS, OWPolyviz, OWSieveMultigram, OWScatterPlot3D, OWRadviz, OWCalibrationPlot, OWParallelCoordinates, OWCorrespondenceAnalysis, OWNxExplorer3D, OWRadvizQt, OWROC, OWDistributionsQt, OWPolyvizQt.
The following prototype widgets could not be imported and will not be available: OWPerformanceCurves, OWCorrelations, OWRScript, OWTimeDataVisualizer, OWCalibratedClassifier.

Unhandled exception of type AttributeError occured at 15:38:21:
Traceback:
  File: orngCanvas.pyw, line 768 in menuItemAboutOrange
  Code: dlg = orngDlgs.AboutDlg(self)
    File: orngDlgs.py, line 1271 in __init__
    Code: hg_revision = version.hg_revision
      AttributeError: 'module' object has no attribute 'hg_revision' 

Unhandled exception of type AttributeError occured at 15:42:06:
Traceback:
  File: orngCanvas.pyw, line 768 in menuItemAboutOrange
  Code: dlg = orngDlgs.AboutDlg(self)
    File: orngDlgs.py, line 1271 in __init__
    Code: hg_revision = version.hg_revision
      AttributeError: 'module' object has no attribute 'hg_revision' 

Unhandled exception of type AttributeError occured at 15:48:54:
Traceback:
  File: orngCanvas.pyw, line 768 in menuItemAboutOrange
  Code: dlg = orngDlgs.AboutDlg(self)
    File: orngDlgs.py, line 1271 in __init__
    Code: hg_revision = version.hg_revision
      AttributeError: 'module' object has no attribute 'hg_revision' 

I guess there are several missing dependencies, but the docs didn't provide the exact list.

There is a problem while import Unicode file using File widget, when viewing it in DataTable widget the encoding is incorrect.

The LibSVM FAQ contains instructions for compiling it to use multiple cores:
http://www.csie.ntu.edu.tw/~cjlin/libsvm/faq.html#f432

This does work as advertised and uses all the cores on a machine for SVM training. Can the copy of LibSVM that Orange includes be modified to use OMP too?

Use case: Linear regression

• take a suitable dataset (more than 1 predictor variables, 1 response variable (to be predicted))
• do a regression with only 1 predictor variable
• do a regression with all the predicotor variables

in test learners they will show the same performance scores results (ie the results of the full regression,
i suspect because of the data feed for test learners), so the performance scores of the regression with 1 only variable are false

as a check showing the regression statistics for each regression method does show the correct data

version 2.7.8

I am using Ubuntu 16.04.1 LTS and installed Orange with the following commands:
sudo apt-get install python3-pip
sudo pip3 install orange3
sudo apt install python3-pyqt5
sudo apt install python3-pyqt5.qtwebkit
sudo apt install python3-pyqt5.qtsvg
sudo pip3 install psycopg2

Then I run orange-canvas and add SQL widget. It draws warning icon and when I open it, it says:
invalid port number: "None"

This can be solved if you enter this to the "server field":
127.0.0.1:5432

My suggestion is if there is no port specified from the user, Orange should use default port (5432), or - there should be another field named port in SQL widget.

And there is another problem: SQL widget says "permission denied to create extension "tsm_system_time".
The problem is, if I connect to psql as postgres user and say CREATE EXTENSION tsm_system_time;, I got an error: extension "tsm_system_time" already exists.

It seems this extension is already installed. Any idea how to solve this?

Dear Sir/Mam,
I am rebuilding orange biolab using cuda, but i am facing a difficulty in replacing the blas library, can anyone tell me where the functions of blas library is used in whole software. as it will help me in achieveing the parallization required

Scam complaint received from slice wallet

SbJsmsH2DF5cQsTNrfWHyVvKQrJ7NqRrXc
Funds were removed on July 29 and
They were never deposited to bank account, Bank of America

Funds were transferred to wallet

Shjn1gLPKF6n1Et9uFFmsorx4x5Sdi8qJH
Incorrectly, need to return funds to clients slice wallet for bank deposit

Hi, is there any problem for generating a windows 64 binary distribution or the snapshot ?

Thanks,
Jose

Is there a way to get some kind of error measurement (eg: standard deviation, confidence interval) of the AUC after doing cross validations? It would be helpful to get a list of all such values from doing cross validations instead of just a single AUC.

The relevant functions are AUC(test_results=None, multiclass=0, ignore_weights=False) and cross_validation(learners, examples, folds=10, stratified=StratifiedIfPossible, preprocessors=(), random_generator=0, callback=None, store_classifiers=False, store_examples=False).

When creating a new column by subtracting two continous variables zero is given as a result.

Widgets used:
predictions + select attributes + feature + data table to check

No matter what values I pass in for Orange.classification.svm.SVMLearner weight I get the same confusion matrix out.

I have 5 classes. And have tried weight being proportional to C (as per LibSVM) and so passed:
weight=[1.0, 1.0, 1.0, 1.0, 1.0]

And weight being absolute (same as the C value I use):
weight=[8.0, 8.0, 8.0, 8.0, 8.0]

Those values and all other values I've tried produce the same confusion matrix which is wildly different from the confusion matrix I get without passing weight values. So I don't think this is working.

I have tried to trace the code but I end up at set_weights in what I think is a compiled C .so file.

After adding Continuize widget into my ows scheme and saving the scheme file corrupts the scheme file:

• The file size increases dramaticallly. For my case it was from 170KB to 7.1MB
• When I try to reopen the scheme file, orange crashes; "segmentation fault (core dumped)"

Then I opened the scheme file in a text editor and I noticed that for Continuize widget properties there are very long and garbage like entries. When I delete the properties entry for Continuize widget and save the scheme then Orange was able to load the scheme.

Example for garbage like entry:
(dbS'\xee\n\x00\x00\x00\x00\x00\x9aB\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x04\xbd\x01\x00\x00\x00\x00\x18B\x00\x00\x00\x00@@\x03\x00\x00\x00\x00\x05\xbd\x01\x00\x00\x00\x00\x00B\x00\x00\x00\x80?@\x03\x00\x00\x00\x00\x06\xbd\x01\x00\x00\x00\x00\x8cB\x00\x00\x00\x00\x00@\x03\x00\x00\x00\x00\x07\xbd\x01\x00\x00\x00\x00\x88A\x00\x00\x00\x00\x00@\x03\x00\x00\x00\x00\x08\xbd\x01\x00\x00\x00\x00\x98B\x00\x00\x00\x00\x00@\x03\x00\x00\x00\x00\t\xbd\x01\x00\x00\x00\x00,B\x00\x00\x00\x00@@\x03\x00\x00\x00\x00\n\xbd\x01\x00\x00\x00\x00\xaaB\x00\x00\x00\x80?@\x03\x00\x00\x00\x00\x0b\xbd\x01\x00\x00\x00\x00tB\x00\x00\x00\x00\x00@\x03\x00\x00\x00\x00\x0c\xbd\x01\x00\x00\x00\x00\xb8A\x00\x00\x00\x80@@\x04\x00\x00\x00\x00\r\xbd\x01\x00\x00\x00\x00tB\x00\x00\x00@@@\x04\x00\x00\x00\x00\x0e\xbd\x01\x00\x00\x00\x00\xe0A\x00\x00\x00@@@\x04\x00\x00\x00\x00\x0f\xbd\x01\x00\x00\x00\x00\x08B\x00\x00\x00\x80@@\x04\x00\x00\x00\x00\x10\xbd\x01\x00\x00\x00\x00\x10B\x00\x00\x00\x80@@\x04\x00\x00\x00\x00\x11\xbd\x01\x00\x00\x00\x00\x10B\x00\x00\x00\x80@@\x04\x00\x00\x00\x00\x12\xbd\x01\x00\x00\x00\x00\x98B\x00\x00\x00@@@\x05\x00\x00\x00\x00\x13\xbd\x01\x00\x00\x00\x00\x18B\x00\x00\x00@@@\x05\x00\x00\x00\x00\x14\xbd\x01\x00\x00\x00\x00pA\x00\x00\x00\x00@@\x05\x00\x00\x00\x00\x15\xbd\x01\x00\x00\x00\x00\x10B\x00\x00\x00@@@\x05\x00\x00\x00\x00\x16\xbd\x01\x00\x00\x00\x00\xc8A\x00\x00\x00\xa0@@\x05\x00\x00\x00\x00\x17\xbd\x01\x00\x00\x00\x00(B\x00\x00\x00\x80@@\x05\x00\x00\x00\x00\x18\xbd\x01\x00\x00\x00\x00\x08B\x00\x00\x00\x80@@\x05\x00\x00\x00\x00\x19\xbd\x01\x00\x00\x00\x00\x08B\x00\x00\x00\x80@@\x05\x00\x00\x00\x00\x1a\xbd\x01\x00\x00\x00\x00\xd8A\x00\x00\x00@@@\x05\x00\x00\x00\x00\x1b\xbd\x01\x00\x00\x00\x00\x00B\x00\x00\x00\x00@@\x05\x00\x00\x00\x00\x1c\xbd\x01\x00\x00\x00\x00\x90B\x00\x00\x00\x80?@\x05\x00\x00\x00\x00\x1d\xbd\x01\x00\x00\x00\x00\xa0A\x00\x00\x00@@@\x05\x00\x00\x00\x00\x1e\xbd\x01\x00\x00\x00\x00@B\x00\x00\x00@@@\x05\x00\x00\x00\x00\x1f\xbd\x01\x00\x00\x00\x00\xe8A\x00\x00\x00\x80@@\x05\x00\x00\x00\x00 \xbd\x01\x00\x00\x00\x00(B\x00\x00\x00\x80@@\x05\x00\x00\x00\x00!\xbd\x01\x00\x00\x00\x00\x08B\x00\x00\x00\x80@@\x05\x00\x00\x00\x00"\xbd\x01\x00\x00\x00\x00\xc0A\x00\x00\x00@@@\x05\x00\x00\x00\x00#\xbd\x01\x00\x00\x00\x00\x96B\x00\x00\x00@@@\x05\x00\x00\x00\x00$\xbd\x01\x00\x00\x00\x00\xb8A\x00\x00\x00\xe0@@\x05\x00\x00\x00\x00%\xbd\x01\x00\x00\x00\x00\x08B\x00\x00\x00@@@\x05\x00\x00\x00\x00&\xbd\x01\x00\x00\x00\x00\x98A\x00\x00\x00\x80@@\x05\x00\x00\x00\x00'\xbd\x01\x00\x00\x00\x00<B\x00\x00\x00@@@\x05\x00\x00\x00\x00(\xbd\x01\x00\x00\x00\x00\x00B\x00\x00\x00@@@\x05\x00\x00\x00\x00)\xbd\x01\x00\x00\x00\x00\x0cB\x00\x00\x00@@@\x05\x00\x00\x00\x00*\xbd\x01\x00\x00\x00\x00\x96B\x00\x00\x00@@@\x05\x00\x00\x00\x00+\xbd\x01\x00\x00\x00\x00\x90A\x00\x00\x00@@@\x05\x00\x00\x00\x00,\xbd\x01\x00\x00\x00\x00\xc8A\x00\x00\x00@@@\x05\x00\x00\x00\x00-

I was trying to create data tables from Python list of list. I found that there was a problem with importing the values correctly for some relatively large numbers. It seemed that there was bug when creating a Continunous Value with relatively large numbers. For example

Orange.data.Value(Orange.feature.Continuous(),308632021)

This construction will give me the following Value:
<orange.Value ''='308632032.000'>

It seems that for relatively large numbers, the conversion would usually be wrong but in a way that is not like an overflow.

Hi all,
I'm trying to use the SQLReader class in python script widget to access a sqlite database placed in a different path than orange itself. Here's the code:

from Orange.data.sql import *
r = SQLReader()
r.connect('sqlite:///d:/path/to/database.db/')

and this is the log:

Running script:
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "<string>", line 4, in <module>
  File "[...]\Orange\utils\__init__.py", line 214, in wrap_call
    return func(*args, **kwargs)
  File "[...]\Orange\data\sql.py", line 195, in connect
    (self.quirks, self.conn) = _connection(uri)
  File "[...]\Orange\data\sql.py", line 141, in _connection
    return (quirks, dbmod.connect(host))
ValueError: database parameter must be string or APSW Connection object

Looking at the source code it seem that the connection string is not treated at it should since
line 15 is handling the third slash incorrectly.

I am using orange 3.3.9 for Mac. I am unable to save a classifier (random forest regression). After selecting a filename and a directory the save file button is still grey.

I recently installed Orange 3.2 and I noticed that Orange Canvas does not contain an Associate tab - the one for frequent patterns and such. I checked in the Python terminal that the library is there but there is no way to use it in the GUI interface. I looked around in the options to no avail.

I know this is present in the 2.x version of Orange. Can someone explain why it is missing in 3.2? Is it a bug?

For information, I am using Windows 10.

I am trying to load the titanic dataset from the example datasets given with Orange and build a mosaic plot with it. After I select all the data from the DataTable the Output window pops-up and I get the error below. I am using version 3.2.dev0+ee85297 in Windows7 x64. Orange was installed with Python 3.4 32bits that was pre-existing in my machine

unable to set <Orange.widgets.gui.OrangeComboBox object at 0x04E6E6C0> to value 'Feature 9'. Possible values are status, age, sex, survived.
--------------------------------------------------------------------------------
KeyError                                      Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 690, in process_signals_for_widget
    widget.handleNewSignals()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 396, in handleNewSignals
    self.updateGraphAndPermList()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 447, in updateGraphAndPermList
    self.updateGraph(**args)
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 483, in updateGraph
    data = data[:, attrList + [data.domain.class_var]]
  File "C:\Python34\lib\site-packages\Orange\data\table.py", line 637, in __getitem__
    attributes, col_indices = self.domain._compute_col_indices(col_idx)
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in _compute_col_indices
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in <listcomp>
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 213, in __getitem__
    idx = self._indices[idx]
KeyError: 'Feature 9'
--- Logging error ---
Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 690, in process_signals_for_widget
    widget.handleNewSignals()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 396, in handleNewSignals
    self.updateGraphAndPermList()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 447, in updateGraphAndPermList
    self.updateGraph(**args)
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 483, in updateGraph
    data = data[:, attrList + [data.domain.class_var]]
  File "C:\Python34\lib\site-packages\Orange\data\table.py", line 637, in __getitem__
    attributes, col_indices = self.domain._compute_col_indices(col_idx)
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in _compute_col_indices
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in <listcomp>
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 213, in __getitem__
    idx = self._indices[idx]
KeyError: 'Feature 9'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Python34\lib\logging\__init__.py", line 980, in emit
    stream.write(msg)
AttributeError: 'NoneType' object has no attribute 'write'
Call stack:
  File "C:\Python34\lib\runpy.py", line 170, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\Python34\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Python34\lib\site-packages\Orange\canvas\__main__.py", line 403, in <module>
    sys.exit(main())
  File "C:\Python34\lib\site-packages\Orange\canvas\__main__.py", line 386, in main
    status = app.exec_()
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 714, in event
    return SignalManager.event(self, event)
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\signalmanager.py", line 452, in event
    self.process_queued(max_nodes=1)
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\signalmanager.py", line 316, in process_queued
    self.process_node(node)
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\signalmanager.py", line 335, in process_node
    self.send_to_node(node, signals_in)
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 632, in send_to_node
    self.process_signals_for_widget(node, widget, signals)
  File "C:\Python34\lib\site-packages\Orange\canvas\scheme\widgetsscheme.py", line 694, in process_signals_for_widget
    node.title)
Message: "Error calling 'handleNewSignals()' of '%s'"
Arguments: ('Mosaic Display',)
--------------------------------------------------------------------------------
KeyError                                      Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 321, in resizeEvent
    self.updateGraph()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 483, in updateGraph
    data = data[:, attrList + [data.domain.class_var]]
  File "C:\Python34\lib\site-packages\Orange\data\table.py", line 637, in __getitem__
    attributes, col_indices = self.domain._compute_col_indices(col_idx)
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in _compute_col_indices
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in <listcomp>
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 213, in __getitem__
    idx = self._indices[idx]
KeyError: 'Feature 9'
--------------------------------------------------------------------------------
KeyError                                      Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 325, in showEvent
    self.updateGraph()
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 483, in updateGraph
    data = data[:, attrList + [data.domain.class_var]]
  File "C:\Python34\lib\site-packages\Orange\data\table.py", line 637, in __getitem__
    attributes, col_indices = self.domain._compute_col_indices(col_idx)
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in _compute_col_indices
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in <listcomp>
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 213, in __getitem__
    idx = self._indices[idx]
KeyError: 'Feature 9'
--------------------------------------------------------------------------------
KeyError                                      Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\Orange\widgets\gui.py", line 2550, in __call__
    self.f(**kwds)
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 447, in updateGraphAndPermList
    self.updateGraph(**args)
  File "C:\Python34\lib\site-packages\Orange\widgets\visualize\owmosaic.py", line 483, in updateGraph
    data = data[:, attrList + [data.domain.class_var]]
  File "C:\Python34\lib\site-packages\Orange\data\table.py", line 637, in __getitem__
    attributes, col_indices = self.domain._compute_col_indices(col_idx)
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in _compute_col_indices
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 391, in <listcomp>
    attributes = [self[col] for col in col_idx]
  File "C:\Python34\lib\site-packages\Orange\data\domain.py", line 213, in __getitem__
    idx = self._indices[idx]
KeyError: 'Feature 9'