[chimerax-users] Errors hold when Plugin a bundle into ChimeraX toolshed

Tue Apr 6 16:33:20 PDT 2021

Hello Tom,

I understand now. Thank you very much for your clarification.

Best regards,
Yongcheng

On Tue, Apr 6, 2021 at 5:53 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Yongcheng,
>
>   ChimeraX is just using pip to install your DLStudio wheel file and pip
> sees that it lists a dependency on quadprog from PyPi so it fetches that.
> This is just normal pip install behavior.  But for whatever reason it
> cannot find your C++ compiler on Windows so the pip install of quadprog
> fails.  To debug this I suggest installing Python 3 on your Windows machine
> and trying a "pip install quadprog" and see if that fails -- I assume it
> will, possibly because it cannot find your Visual Studio or considers it
> not compatible with what quadprog requires.
>
>   You should be able to get quadprog to compile on Windows with some
> effort to figure out why pip is unhappy.
>
>   If you are creating this DLstruct plugin to distribute to others for
> example on ChimeraX Toolshed you should be aware that almost no Windows
> users will have a C++ compiler, so quadprog will not install on their
> systems.  The basic problem is the quadprog developers have not provided
> Windows builds on PyPi.  So this will make it unusable in your plugin on
> Windows.  A somewhat painful way to work around this is to compile the
> Windows quadprog yourself and include it in your ChimeraX plugin (as extra
> data files) instead of listing it as a dependency.  Maybe instead you could
> convince the quadprog developer to put a Windows version on PyPi -- as it
> is now it simply is not usable on Windows for the majority of users who do
> not develop their own C++ code.
>
> Tom
>
>
> On Apr 6, 2021, at 12:07 PM, Yongcheng MU <ymu004 at odu.edu> wrote:
>
> Hello Tom,
>
> Thank you so much for your reply.
>
> Yes, I am developing this DLstruct Plugin. I have some other questions:
>
>     1. I have Visual studio code (attached below). Do I still need to
> install Visual Studio 2019 to use instead of Visual Studio Code
>     2. How does ChimeraX find the required packages? In my understanding,
> if ChimeraX couldn't find a required package in the system, it will install
> the package automatically by using pip, is that correct?
> Thank you for your time.
>
> Best regards,
> Yongcheng
>
> * (C++ 14 in the Visual Studio code APP)*
> [image: Screen Shot 2021-04-06 at 2.00.04 PM.png]
>
> *(Bundle info and Dependencies)*
> [image: Screen Shot 2021-04-06 at 2.00.35 PM.png]
>
> On Tue, Apr 6, 2021 at 1:53 PM Tom Goddard <goddard at sonic.net> wrote:
>
>> Hi Yongcheng,
>>
>>   Did you develop this DLStruct plugin?  I have not seen it before.  The
>> error message says it was trying to install the quadprog package from PyPi,
>> I guess a quadratic programming library.  You can see on PyPi that it only
>> has a source code distribution
>>
>> https://pypi.org/project/quadprog/#files
>>
>> and your error indicates it needs to be compiled with Microsoft Visual
>> C++ compilers which you apparently do not have installed.
>>
>>
>> *building 'quadprog' extension error: Microsoft Visual C++ 14.0 is
>> required. Get it with "Build Tools for Visual
>> Studio": https://visualstudio.microsoft.com/downloads/
>> <https://visualstudio.microsoft.com/downloads/> *
>>
>>
>> You will have to get the C++ compiler to build quadprog on Windows.
>>
>> Tom
>>
>>
>>
>> On Apr 6, 2021, at 8:31 AM, Yongcheng MU <ymu004 at odu.edu> wrote:
>>
>> Hello,
>>
>> Hope this email finds you well.
>>
>> I'm trying to Plugin a bundle into ChimeraX. I have
>> successfully installed a bundle on macOS, now I'm trying to install the
>> bundle on a Window Desktop. It holds some errors, I searched a lot and I
>> failed to fix this issue. I wonder if you have any suggestions?
>>
>> Best regards,
>> Yongcheng
>>
>>
>>
>> [toolshed install Z:/Plugin_dl\dist\ChimeraX_DLStruct-0.1-py3-none-
>> any.whl](cxcmd:toolshed install
>> Z:/Plugin_dl\\dist\\ChimeraX_DLStruct-0.1-py3-none-any.whl)
>>
>> Traceback (most recent call last):
>> File "C:\Program Files\ChimeraX
>> 1.1\bin\lib\site-packages\chimerax\toolshed_utils\__init__.py", line 489,
>> in _pip_install
>> results = _run_pip(command, logger)
>> File "C:\Program Files\ChimeraX
>> 1.1\bin\lib\site-packages\chimerax\toolshed_utils\__init__.py", line 540,
>> in _run_pip
>>
>> *raise RuntimeError(s)RuntimeError: Looking in indexes:
>> https://pypi.org/simple <https://pypi.org/simple>,
>> https://cxtoolshed.rbvi.ucsf.edu/pypi/
>> <https://cxtoolshed.rbvi.ucsf.edu/pypi/> *
>> Processing z:\plugin_dl\dist\chimerax_dlstruct-0.1-py3-none-any.whl
>> Requirement already satisfied: ChimeraX-Core~=1.0 in c:\program
>> files\chimerax 1.1\bin\lib\site-packages (from ChimeraX-DLStruct==0.1)
>> (1.1)
>> Requirement already satisfied: numpy~=1.16.4 in
>> c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from
>> ChimeraX-DLStruct==0.1) (1.16.6)
>> Requirement already satisfied: torch~=1.7.1 in
>> c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from
>> ChimeraX-DLStruct==0.1) (1.7.1)
>> Requirement already satisfied: numpy~=1.16.4 in
>> c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from
>> ChimeraX-DLStruct==0.1) (1.16.6)
>> Requirement already satisfied: typing-extensions in
>> c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from
>> torch~=1.7.1->ChimeraX-DLStruct==0.1) (3.7.4.3)
>> Collecting quadprog~=0.1.7
>> Using cached quadprog-0.1.8.tar.gz (269 kB)
>> Requirement already satisfied: Cython in c:\program files\chimerax
>> 1.1\bin\lib\site-packages (from quadprog~=0.1.7->ChimeraX-DLStruct==0.1)
>> (0.29.20)
>> Collecting importlib-metadata~=0.17
>> Using cached importlib_metadata-0.23-py2.py3-none-any.whl (28 kB)
>> Requirement already satisfied: zipp>=0.5 in
>> c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from
>> importlib-metadata~=0.17->ChimeraX-DLStruct==0.1) (3.4.1)
>>
>>
>>
>>
>> *Building wheels for collected packages: quadprog Building wheel for
>> quadprog (setup.py): started Building wheel for quadprog (setup.py):
>> finished with status 'error' Running setup.py clean for quadprog Failed to
>> build quadprog *
>> Installing collected packages: quadprog, importlib-metadata,
>> ChimeraX-DLStruct
>> Running setup.py install for quadprog: started
>> Running setup.py install for quadprog: finished with status 'error'
>> *ERROR: Command errored out with exit status 1: *
>> command: 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe' -u -c 'import
>> sys, setuptools, tokenize; sys.argv[0] =
>> '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';
>> __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\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\ymu\AppData\Local\Temp\pip-wheel-gloxcthl'
>> cwd:
>> C:\Users\ymu\AppData\Local\Temp\pip-install-xakoctiw\quadprog_7cb25d8bb3904ea3b64643e58389ec80\
>>
>> Complete output (6 lines):
>> running bdist_wheel
>> running build
>> running build_ext
>>
>>
>> *skipping 'quadprog\quadprog.cpp' Cython extension (up-to-date) building
>> 'quadprog' extension error: Microsoft Visual C++ 14.0 is required. Get it
>> with "Build Tools for Visual Studio":
>> https://visualstudio.microsoft.com/downloads/
>> <https://visualstudio.microsoft.com/downloads/> *
>> ----------------------------------------
>>
>>
>> *ERROR: Failed building wheel for quadprog DEPRECATION: Could not build
>> wheels for quadprog which do not use PEP 517. pip will fall back to legacy
>> 'setup.py install' for these. pip 21.0 will remove support for this
>> functionality. A possible replacement is to fix the wheel build issue
>> reported above. You can find discussion regarding this at
>> https://github.com/pypa/pip/issues/8368
>> <https://github.com/pypa/pip/issues/8368>. ERROR: Command errored out with
>> exit status 1: *
>> command: 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe' -u -c 'import
>> sys, setuptools, tokenize; sys.argv[0] =
>> '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';
>> __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\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\ymu\AppData\Local\Temp\pip-record-gcrsp7lk\install-record.txt'
>> --single-version-externally-managed --user --prefix= --compile
>> --install-headers
>> 'C:\Users\ymu\AppData\Local\UCSF\ChimeraX\Python37\Include\quadprog'
>> cwd:
>> C:\Users\ymu\AppData\Local\Temp\pip-install-xakoctiw\quadprog_7cb25d8bb3904ea3b64643e58389ec80\
>>
>> Complete output (6 lines):
>> running install
>> running build
>> running build_ext
>> skipping 'quadprog\quadprog.cpp' Cython extension (up-to-date)
>> building 'quadprog' extension
>> error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools
>> for Visual Studio": https://visualstudio.microsoft.com/downloads/
>> ----------------------------------------
>> ERROR: Command errored out with exit status 1: 'C:\Program Files\ChimeraX
>> 1.1\bin\ChimeraX.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0]
>> =
>> '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';
>> __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\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\ymu\AppData\Local\Temp\pip-record-gcrsp7lk\install-record.txt'
>> --single-version-externally-managed --user --prefix= --compile
>> --install-headers
>> 'C:\Users\ymu\AppData\Local\UCSF\ChimeraX\Python37\Include\quadprog' Check
>> the logs for full command output.
>> WARNING: You are using pip version 20.2.2; however, version 21.0.1 is
>> available.
>> You should consider upgrading via the 'C:\Program Files\ChimeraX
>> 1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command.
>>
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