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

Tue Apr 6 12:07:01 PDT 2021

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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