windows OS installation steps.

Question

windows OS installation steps.

rupav opened this issue 6 years ago · comments

I would like to work on it.

rupav jain · Answer 1 · Wed Feb 14 2018 17:45:46 GMT+0800 (China Standard Time)

@akram-mohammed I want to claim installation on windows( though I am not able to install dependency rpy2 from pip, but found a way around) . Still getting few installation error, but will solve them too eventually.
Can you please add me to https://groups.google.com/forum/#!forum/helikarlab-gsoc .
I have few queries regarding Candis project.

rupav jain · Answer 2 · Wed Feb 14 2018 22:18:08 GMT+0800 (China Standard Time)

cc @achillesrasquinha

Akram Mohammed · Answer 3 · Thu Feb 15 2018 04:58:46 GMT+0800 (China Standard Time)

Rupav, you are a member of the HelikarLab google forum. Thank you, Akram Mohammed, M.S, Ph.D. Postdoctoral Research Associate Computational Systems Biologist Department of Biochemistry University of Nebraska-Lincoln From: rupav jain Sent: Wednesday, February 14, 2018 3:45 AM To: HelikarLab/candis Cc: Akram Mohammed; Mention Subject: Re: [HelikarLab/candis] windows OS installation steps. (#9) @akram-mohammed I want to claim installation on windows( though I am not able to install dependency rpy2 from pip, but found a way around) . Still getting few installation error, but will solve them too eventually. Can you please add me to https://groups.google.com/forum/#!forum/helikarlab-gsoc . I have few queries regarding Candis project. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

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Akram Mohammed · Answer 4 · Thu Feb 15 2018 05:04:01 GMT+0800 (China Standard Time)

Excellent! Looking forward to your proposal. Feel free to ask any questions you may have. Akram Mohammed, M.S, Ph.D. Postdoctoral Research Associate Computational Systems Biologist Department of Biochemistry University of Nebraska-Lincoln From: rupav jain Sent: Wednesday, February 14, 2018 3:42 AM To: HelikarLab/candis Cc: Subscribed Subject: [HelikarLab/candis] windows OS installation steps. (#9) I would like to work on it. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

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Achilles Rasquinha · Answer 5 · Thu Feb 15 2018 22:46:03 GMT+0800 (China Standard Time)

Hi there. That's great! For a start, you can maybe try writing a detailed instruction to have it setup on Windows here. Refer our guide structure for the same.

We're also attempting to have candis as a one command install within this script get-candis. You could start contributing to write one for Windows.

In case of System Dependencies, I notice that Windows has Chocolatey to install. Do let me know what you can come up with!

rupav jain · Answer 6 · Fri Feb 16 2018 01:34:30 GMT+0800 (China Standard Time)

This bug is not solved yet LeeKamentsky/python-javabridge#34, I have installed java, set PATH to bin directory of jdk as well. Able to run java from cmd.

same error occured when I used pip install -r requirements.txt

$ pip install javabridge
Collecting javabridge
  Using cached javabridge-1.0.15.tar.gz
    Complete output from command python setup.py egg_info:
    Failed to find registry entry: SOFTWARE\JavaSoft\Java Runtime Environment
    Traceback (most recent call last):
      File "C:\Users\MARK\AppData\Local\Temp\pip-build-ky_zdpr6\javabridge\javabridge\locate.py", line 131, in find_javahome
        kjava = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, java_key_path)
    FileNotFoundError: [WinError 2] The system cannot find the file specified
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\MARK\AppData\Local\Temp\pip-build-ky_zdpr6\javabridge\setup.py", line 393, in <module>
        ext_modules=ext_modules(),
      File "C:\Users\MARK\AppData\Local\Temp\pip-build-ky_zdpr6\javabridge\setup.py", line 95, in ext_modules
        raise Exception("JVM not found")
    Exception: JVM not found

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\MARK\AppData\Local\Temp\pip-build-ky_zdpr6\javabridge\

@achillesrasquinha @akram-mohammed any suggestions where to look for now?
I am using windows 10 64-bit OS.
PS: I have never used java before.

Achilles Rasquinha · Answer 7 · Fri Feb 16 2018 04:24:44 GMT+0800 (China Standard Time)

Did you try javabridge's latest from the master branch?

Achilles Rasquinha · Answer 8 · Fri Feb 16 2018 04:25:26 GMT+0800 (China Standard Time)

Again, see if you can debug on this steps here. Meant of OS X, but you get the idea.

rupav jain · Answer 9 · Fri Feb 16 2018 11:10:02 GMT+0800 (China Standard Time)

@achillesrasquinha I tried with `pip install -r requirements.txt``(so it clones the javabridge repo and by default master is getting cloned ?) too, now new error are produced:


MARK@DESKTOP-NV34LC4 MINGW64 /d/Rjain/opensource/MyProjects/candis (dev)
$ pip install -r requirements.txt
Collecting addict (from -r requirements.txt (line 1))
  Using cached addict-2.1.2.tar.gz
Requirement already satisfied: PyYAML in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 2))
Requirement already satisfied: requests in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 3))
Requirement already satisfied: numpy in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 5))
Requirement already satisfied: scipy in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 6))
Requirement already satisfied: matplotlib in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 7))
Requirement already satisfied: pandas in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 8))
Requirement already satisfied: seaborn in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 9))
Collecting liac-arff (from -r requirements.txt (line 10))
  Using cached liac-arff-2.1.1.tar.gz
Requirement already satisfied: Cython in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 12))
Collecting javabridge from git+https://github.com/LeeKamentsky/python-javabridge.git#egg=javabridge (from -r requirements.txt (line 13))
  Cloning https://github.com/LeeKamentsky/python-javabridge.git to c:\users\mark\appdata\local\temp\pip-build-bp_tyuy0\javabridge
Collecting python-weka-wrapper3 (from -r requirements.txt (line 14))
  Using cached python-weka-wrapper3-0.1.3.tar.gz
Collecting pygraphviz (from -r requirements.txt (line 15))
  Downloading pygraphviz-1.3.1.zip (123kB)
Requirement already satisfied: Pillow in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 16))
Requirement already satisfied: Flask in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 18))
Collecting django-htmlmin (from -r requirements.txt (line 19))
  Using cached django_htmlmin-0.10.0-py2.py3-none-any.whl
Collecting Flask-SocketIO (from -r requirements.txt (line 20))
  Downloading Flask_SocketIO-2.9.3-py2.py3-none-any.whl
Collecting redis (from -r requirements.txt (line 21))
  Downloading redis-2.10.6-py2.py3-none-any.whl (64kB)
Collecting rq (from -r requirements.txt (line 22))
  Downloading rq-0.10.0-py2.py3-none-any.whl (53kB)
Requirement already satisfied: gunicorn in c:\users\mark\anaconda3\lib\site-packages (from -r requirements.txt (line 23))
Requirement already satisfied: idna<2.7,>=2.5 in c:\users\mark\anaconda3\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: urllib3<1.23,>=1.21.1 in c:\users\mark\anaconda3\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: certifi>=2017.4.17 in c:\users\mark\anaconda3\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in c:\users\mark\anaconda3\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: six>=1.10 in c:\users\mark\anaconda3\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: python-dateutil in c:\users\mark\anaconda3\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: pytz in c:\users\mark\anaconda3\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: cycler>=0.10 in c:\users\mark\anaconda3\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in c:\users\mark\anaconda3\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: olefile in c:\users\mark\anaconda3\lib\site-packages (from Pillow->-r requirements.txt (line 16))
Requirement already satisfied: itsdangerous>=0.21 in c:\users\mark\anaconda3\lib\site-packages (from Flask->-r requirements.txt (line 18))
Requirement already satisfied: Werkzeug>=0.7 in c:\users\mark\anaconda3\lib\site-packages (from Flask->-r requirements.txt (line 18))
Requirement already satisfied: Jinja2>=2.4 in c:\users\mark\anaconda3\lib\site-packages (from Flask->-r requirements.txt (line 18))
Requirement already satisfied: click>=2.0 in c:\users\mark\anaconda3\lib\site-packages (from Flask->-r requirements.txt (line 18))
Requirement already satisfied: html5lib in c:\users\mark\anaconda3\lib\site-packages (from django-htmlmin->-r requirements.txt (line 19))
Requirement already satisfied: beautifulsoup4 in c:\users\mark\anaconda3\lib\site-packages (from django-htmlmin->-r requirements.txt (line 19))
Collecting python-socketio>=1.6.1 (from Flask-SocketIO->-r requirements.txt (line 20))
  Downloading python_socketio-1.8.4-py2.py3-none-any.whl
Requirement already satisfied: MarkupSafe>=0.23 in c:\users\mark\anaconda3\lib\site-packages (from Jinja2>=2.4->Flask->-r requirements.txt (line 18))
Collecting python-engineio>=1.2.1 (from python-socketio>=1.6.1->Flask-SocketIO->-r requirements.txt (line 20))
  Downloading python_engineio-2.0.2-py2.py3-none-any.whl
Building wheels for collected packages: addict, liac-arff, python-weka-wrapper3, pygraphviz
  Running setup.py bdist_wheel for addict: started
  Running setup.py bdist_wheel for addict: finished with status 'done'
  Stored in directory: C:\Users\MARK\AppData\Local\pip\Cache\wheels\2d\1e\af\6d08d13681e5dd59a3ce436a15ffec3bbe40d6bb7b68866353
  Running setup.py bdist_wheel for liac-arff: started
  Running setup.py bdist_wheel for liac-arff: finished with status 'done'
  Stored in directory: C:\Users\MARK\AppData\Local\pip\Cache\wheels\fa\05\89\ad13dcf092046e2ea86beec50db9ad5ce8a3ba0c4d00489579
  Running setup.py bdist_wheel for python-weka-wrapper3: started
  Running setup.py bdist_wheel for python-weka-wrapper3: finished with status 'done'
  Stored in directory: C:\Users\MARK\AppData\Local\pip\Cache\wheels\b5\71\96\55c6e303d164c26ca0a5e2a5bf509c0997007af6684527212c
  Running setup.py bdist_wheel for pygraphviz: started
  Running setup.py bdist_wheel for pygraphviz: finished with status 'error'
  Complete output from command C:\Users\MARK\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-bp_tyuy0\\pygraphviz\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d C:\Users\MARK\AppData\Local\Temp\tmpcm8r554upip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.6
  creating build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\agraph.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\graphviz.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\release.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\version.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\__init__.py -> build\lib.win-amd64-3.6\pygraphviz
  creating build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_attribute_defaults.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_clear.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_drawing.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_edge_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_graph.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_html.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_layout.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_node_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_readwrite.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_string.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_subgraph.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_unicode.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\__init__.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  running egg_info
  writing pygraphviz.egg-info\PKG-INFO
  writing dependency_links to pygraphviz.egg-info\dependency_links.txt
  writing top-level names to pygraphviz.egg-info\top_level.txt
  reading manifest file 'pygraphviz.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '*~' found anywhere in distribution
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '.svn' found anywhere in distribution
  no previously-included directories found matching 'doc\build'
  writing manifest file 'pygraphviz.egg-info\SOURCES.txt'
  copying pygraphviz\graphviz.i -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\graphviz_wrap.c -> build\lib.win-amd64-3.6\pygraphviz
  running build_ext
  building 'pygraphviz._graphviz' extension
  error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": http://landinghub.visualstudio.com/visual-cpp-build-tools

  ----------------------------------------
  Failed building wheel for pygraphviz
  Running setup.py clean for pygraphviz
Successfully built addict liac-arff python-weka-wrapper3
Failed to build pygraphviz
Installing collected packages: addict, liac-arff, javabridge, python-weka-wrapper3, pygraphviz, django-htmlmin, python-engineio, python-socketio, Flask-SocketIO, redis, rq
  Running setup.py install for javabridge: started
    Running setup.py install for javabridge: finished with status 'error'
    Complete output from command C:\Users\MARK\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-bp_tyuy0\\javabridge\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MARK\AppData\Local\Temp\pip-xi29j9sl-record\install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.6
    creating build\lib.win-amd64-3.6\javabridge
    copying javabridge\jutil.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\locate.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\noseplugin.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\wrappers.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\_version.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\__init__.py -> build\lib.win-amd64-3.6\javabridge
    creating build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_cpython.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_javabridge.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_jutil.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_wrappers.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\__init__.py -> build\lib.win-amd64-3.6\javabridge\tests
    creating build\lib.win-amd64-3.6\javabridge\jars
    copying javabridge\jars\rhino-1.7R4.jar -> build\lib.win-amd64-3.6\javabridge\jars
    running build_ext
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java\org\cellprofiler\runnablequeue\RunnableQueue.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\build\lib.win-amd64-3.6\javabridge\jars\runnablequeue.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/runnablequeue/RunnableQueue$1.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/runnablequeue/RunnableQueue.class
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java\org\cellprofiler\javabridge\test\RealRect.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\build\lib.win-amd64-3.6\javabridge\jars\test.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/test/RealRect.class
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java\org\cellprofiler\javabridge\CPython.java C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    Note: C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java uses unchecked or unsafe operations.
    Note: Recompile with -Xlint:unchecked for details.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\build\lib.win-amd64-3.6\javabridge\jars\cpython.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/CPython$StackFrame.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/CPython$WrappedException.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/CPython.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\java org/cellprofiler/javabridge/CPythonInvocationHandler.class
    building 'javabridge._javabridge' extension
    error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": http://landinghub.visualstudio.com/visual-cpp-build-tools

    ----------------------------------------
Command "C:\Users\MARK\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-bp_tyuy0\\javabridge\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MARK\AppData\Local\Temp\pip-xi29j9sl-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\MARK\AppData\Local\Temp\pip-build-bp_tyuy0\javabridge\

Will try solving this in evening.

Achilles Rasquinha · Answer 10 · Fri Feb 16 2018 20:17:34 GMT+0800 (China Standard Time)

Try updating Visual C++

Also, looks like you're working on a conda env. Let us know what you discover.

Achilles Rasquinha · Answer 11 · Sat Feb 17 2018 14:39:14 GMT+0800 (China Standard Time)

Hi Rupav, unfortunately. I've got a Mac for setup + Ubuntu, CentOS (I have not tried this on it yet, and will work on this, would love to collaborate). Got a daytime job! :)

If there's anyway I can help to debug, do let me know.

rupav jain · Answer 12 · Sat Feb 17 2018 16:01:01 GMT+0800 (China Standard Time)

$ pip install -r requirements.txt
Requirement already satisfied: addict in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 1))
Requirement already satisfied: PyYAML in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 2))
Requirement already satisfied: requests in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 3))
Requirement already satisfied: numpy in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 5))
Requirement already satisfied: scipy in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 6))
Requirement already satisfied: matplotlib in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 7))
Requirement already satisfied: pandas in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 8))
Requirement already satisfied: seaborn in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 9))
Requirement already satisfied: liac-arff in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 10))
Requirement already satisfied: Cython in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from -r requirements.txt (line 12))
Collecting javabridge from git+https://github.com/LeeKamentsky/python-javabridge.git#egg=javabridge (from -r requirements.txt (line 13))
  Cloning https://github.com/LeeKamentsky/python-javabridge.git to c:\users\mark\appdata\local\temp\pip-build-a91xz_y8\javabridge
Collecting python-weka-wrapper3 (from -r requirements.txt (line 14))
Collecting pygraphviz (from -r requirements.txt (line 15))
  Using cached pygraphviz-1.3.1.zip
Collecting Pillow (from -r requirements.txt (line 16))
  Using cached Pillow-5.0.0-cp36-cp36m-win_amd64.whl
Collecting Flask (from -r requirements.txt (line 18))
  Using cached Flask-0.12.2-py2.py3-none-any.whl
Collecting django-htmlmin (from -r requirements.txt (line 19))
  Using cached django_htmlmin-0.10.0-py2.py3-none-any.whl
Collecting Flask-SocketIO (from -r requirements.txt (line 20))
  Using cached Flask_SocketIO-2.9.3-py2.py3-none-any.whl
Collecting redis (from -r requirements.txt (line 21))
  Using cached redis-2.10.6-py2.py3-none-any.whl
Collecting rq (from -r requirements.txt (line 22))
  Using cached rq-0.10.0-py2.py3-none-any.whl
Collecting gunicorn (from -r requirements.txt (line 23))
  Using cached gunicorn-19.7.1-py2.py3-none-any.whl
Requirement already satisfied: certifi>=2017.4.17 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: urllib3<1.23,>=1.21.1 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: idna<2.7,>=2.5 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from requests->-r requirements.txt (line 3))
Requirement already satisfied: cycler>=0.10 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: six>=1.10 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: python-dateutil>=2.1 in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Requirement already satisfied: pytz in d:\rjain\opensource\myprojects\candisvenv\lib\site-packages (from matplotlib->-r requirements.txt (line 7))
Collecting click>=2.0 (from Flask->-r requirements.txt (line 18))
  Using cached click-6.7-py2.py3-none-any.whl
Collecting itsdangerous>=0.21 (from Flask->-r requirements.txt (line 18))
Collecting Werkzeug>=0.7 (from Flask->-r requirements.txt (line 18))
  Using cached Werkzeug-0.14.1-py2.py3-none-any.whl
Collecting Jinja2>=2.4 (from Flask->-r requirements.txt (line 18))
  Using cached Jinja2-2.10-py2.py3-none-any.whl
Collecting html5lib (from django-htmlmin->-r requirements.txt (line 19))
  Using cached html5lib-1.0.1-py2.py3-none-any.whl
Collecting beautifulsoup4 (from django-htmlmin->-r requirements.txt (line 19))
  Using cached beautifulsoup4-4.6.0-py3-none-any.whl
Collecting python-socketio>=1.6.1 (from Flask-SocketIO->-r requirements.txt (line 20))
  Using cached python_socketio-1.8.4-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.4->Flask->-r requirements.txt (line 18))
Collecting webencodings (from html5lib->django-htmlmin->-r requirements.txt (line 19))
  Using cached webencodings-0.5.1-py2.py3-none-any.whl
Collecting python-engineio>=1.2.1 (from python-socketio>=1.6.1->Flask-SocketIO->-r requirements.txt (line 20))
  Using cached python_engineio-2.0.2-py2.py3-none-any.whl
Building wheels for collected packages: pygraphviz
  Running setup.py bdist_wheel for pygraphviz: started
  Running setup.py bdist_wheel for pygraphviz: finished with status 'error'
  Complete output from command d:\rjain\opensource\myprojects\candisvenv\scripts\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-a91xz_y8\\pygraphviz\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d C:\Users\MARK\AppData\Local\Temp\tmp2_5vxhztpip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.6
  creating build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\agraph.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\graphviz.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\release.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\version.py -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\__init__.py -> build\lib.win-amd64-3.6\pygraphviz
  creating build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_attribute_defaults.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_clear.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_drawing.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_edge_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_graph.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_html.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_layout.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_node_attributes.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_readwrite.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_string.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_subgraph.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\test_unicode.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  copying pygraphviz\tests\__init__.py -> build\lib.win-amd64-3.6\pygraphviz\tests
  running egg_info
  writing pygraphviz.egg-info\PKG-INFO
  writing dependency_links to pygraphviz.egg-info\dependency_links.txt
  writing top-level names to pygraphviz.egg-info\top_level.txt
  reading manifest file 'pygraphviz.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '*~' found anywhere in distribution
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '.svn' found anywhere in distribution
  no previously-included directories found matching 'doc\build'
  writing manifest file 'pygraphviz.egg-info\SOURCES.txt'
  copying pygraphviz\graphviz.i -> build\lib.win-amd64-3.6\pygraphviz
  copying pygraphviz\graphviz_wrap.c -> build\lib.win-amd64-3.6\pygraphviz
  running build_ext
  building 'pygraphviz._graphviz' extension
  error: [WinError 3] The system cannot find the path specified: 'C:\\Program Files (x86)\\VisualStudios\\VC\\Tools\\MSVC\\14.12.25827\\PlatformSDK\\lib'

  ----------------------------------------
  Failed building wheel for pygraphviz
  Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: javabridge, python-weka-wrapper3, pygraphviz, Pillow, click, itsdangerous, Werkzeug, MarkupSafe, Jinja2, Flask, webencodings, html5lib, beautifulsoup4, django-htmlmin, python-engineio, python-socketio, Flask-SocketIO, redis, rq, gunicorn
  Running setup.py install for javabridge: started
    Running setup.py install for javabridge: finished with status 'error'
    Complete output from command d:\rjain\opensource\myprojects\candisvenv\scripts\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-a91xz_y8\\javabridge\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MARK\AppData\Local\Temp\pip-7vohty6r-record\install-record.txt --single-version-externally-managed --compile --install-headers d:\rjain\opensource\myprojects\candisvenv\include\site\python3.6\javabridge:
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.6
    creating build\lib.win-amd64-3.6\javabridge
    copying javabridge\jutil.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\locate.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\noseplugin.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\wrappers.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\_version.py -> build\lib.win-amd64-3.6\javabridge
    copying javabridge\__init__.py -> build\lib.win-amd64-3.6\javabridge
    creating build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_cpython.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_javabridge.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_jutil.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\test_wrappers.py -> build\lib.win-amd64-3.6\javabridge\tests
    copying javabridge\tests\__init__.py -> build\lib.win-amd64-3.6\javabridge\tests
    creating build\lib.win-amd64-3.6\javabridge\jars
    copying javabridge\jars\rhino-1.7R4.jar -> build\lib.win-amd64-3.6\javabridge\jars
    running build_ext
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java\org\cellprofiler\runnablequeue\RunnableQueue.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\build\lib.win-amd64-3.6\javabridge\jars\runnablequeue.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/runnablequeue/RunnableQueue$1.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/runnablequeue/RunnableQueue.class
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java\org\cellprofiler\javabridge\test\RealRect.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\build\lib.win-amd64-3.6\javabridge\jars\test.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/test/RealRect.class
    C:\Program Files\Java\jdk-9.0.4\bin\javac.exe -source 6 -target 6 C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java\org\cellprofiler\javabridge\CPython.java C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java
    warning: [options] bootstrap class path not set in conjunction with -source 1.6
    warning: [options] source value 1.6 is obsolete and will be removed in a future release
    warning: [options] target value 1.6 is obsolete and will be removed in a future release
    warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    Note: C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java uses unchecked or unsafe operations.
    Note: Recompile with -Xlint:unchecked for details.
    4 warnings
    C:\Program Files\Java\jdk-9.0.4\bin\jar.exe cf C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\build\lib.win-amd64-3.6\javabridge\jars\cpython.jar -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/CPython$StackFrame.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/CPython$WrappedException.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/CPython.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/CPythonInvocationHandler.class -C C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\java org/cellprofiler/javabridge/CPythonInvocationHandler.class
    building 'javabridge._javabridge' extension
    error: [WinError 3] The system cannot find the path specified: 'C:\\Program Files (x86)\\VisualStudios\\VC\\Tools\\MSVC\\14.12.25827\\PlatformSDK\\lib'

    ----------------------------------------
Command "d:\rjain\opensource\myprojects\candisvenv\scripts\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MARK\\AppData\\Local\\Temp\\pip-build-a91xz_y8\\javabridge\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MARK\AppData\Local\Temp\pip-7vohty6r-record\install-record.txt --single-version-externally-managed --compile --install-headers d:\rjain\opensource\myprojects\candisvenv\include\site\python3.6\javabridge" failed with error code 1 in C:\Users\MARK\AppData\Local\Temp\pip-build-a91xz_y8\javabridge\

I was finding solution for previous error, I uninstalled Visual Studio Code in between, and now these error came up, cant get past through it :( . Looking for solutions for hours but not finding any, also not able to instal from conda channel too - pygraphviz .

Achilles Rasquinha · Answer 13 · Sat Feb 17 2018 21:07:45 GMT+0800 (China Standard Time)

Okay. It looks like the issue I had with javabridge has been fixed. I'll try avoiding the master branch installation for now.

rupav jain · Answer 14 · Sun Feb 18 2018 02:49:00 GMT+0800 (China Standard Time)

@achillesrasquinha I am able to run the project on Ubuntu(I have made it guest OS using oracle VM) following the installation instructions (although sudo apt-get install python3-tk was needed as a extra command).
I will try a different approach on windows ASAP for installation.

Achilles Rasquinha · Answer 15 · Sun Feb 18 2018 17:45:35 GMT+0800 (China Standard Time)

Wait for #13 to merged. We'll see what we get next. Removing some redundant stuff for now.

Achilles Rasquinha · Answer 16 · Sun Feb 18 2018 17:50:04 GMT+0800 (China Standard Time)

Do try the get-candis script and let us know what you get!

rupav jain · Answer 17 · Sun Feb 18 2018 19:49:20 GMT+0800 (China Standard Time)

Ok @achillesrasquinha , I will try it ASAP.

rupav jain · Answer 18 · Sun Feb 18 2018 20:08:23 GMT+0800 (China Standard Time)

@achillesrasquinha I am afraid, I have to go through curl, equivalent of bit.do on windows to run get-candis in the very first place . I was looking https://github.com/HelikarLab/candis/wiki/A-Hitchhiker's-Guide-to-Installing-candis-on-Mac-OS-X , which uses get-candis script. If get-candis is a python file, why didn't you put it with .py extension.

Achilles Rasquinha · Answer 19 · Sun Feb 18 2018 21:28:24 GMT+0800 (China Standard Time)

I'd never tested this on a Windows machine. *nix OS don't need an extension, one could use a shebang to launch the executable.

The only reason why this needs a Windows compat is because many users of the application might not have *nix. Otherwise, spawning a VM would not hurt. 😛

Give me some time! As soon as a I get hands on a Windows machine, I'll have this tested.

BTW, get-candis isn't Windows compat. Requires contributors. Try it on your Ubuntu VM.

rupav jain · Answer 20 · Sat Mar 03 2018 22:34:00 GMT+0800 (China Standard Time)

Update: @achillesrasquinha I am busy till 12th March because of college exams, thats why no activity/update nowadays. Will get back to this ASAP, PS: I tried get-candis (around 13 days back) (followed steps similar to Mac OS-X https://github.com/HelikarLab/candis/wiki/A-Hitchhiker's-Guide-to-Installing-candis-on-Mac-OS-X ) but was unsuccessful in setting up on Ubuntu 16.10 .

Samson Okubanjo · Answer 21 · Sat Apr 06 2019 23:33:14 GMT+0800 (China Standard Time)

@rupav Were you able to install this on your windows computer? I am having troubles installing it because of a dependency (pygraphviz).

If you were able to, what steps didi you take? The Hitchhiker's guide isn't updated yet too.

Cc @akram-mohammed

rupav jain · Answer 22 · Sun Apr 07 2019 00:27:55 GMT+0800 (China Standard Time)

It's not window compatible yet @s-okubanjo.

Achilles Rasquinha · Answer 23 · Wed Jul 03 2019 02:44:31 GMT+0800 (China Standard Time)

Kindly use the docker solution provided.