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Simpletraj installation problem #4

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hasanmme opened this issue May 19, 2020 · 4 comments
Open

Simpletraj installation problem #4

hasanmme opened this issue May 19, 2020 · 4 comments

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@hasanmme
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Recently, I am trying to use the PyCGtool for coarse-grain modeling of a long-chain glycan molecule. Simpletraj is required for the PyCGtool. I am having difficulty installing Simpletraj in the windows operating system (Windows 10 64X). I have already installed the dependencies such as Microsoft C++ 14.0. Still, I am getting the error message. The error message is appended below:
Please let me know what causing the problem.
C:>pip install simpletraj

Collecting simpletraj
Using cached simpletraj-0.5.tar.gz (87 kB)
Requirement already satisfied: numpy in c:\users\mahmudk\appdata\local\programs\python\python35\lib\site-packages (from simpletraj) (1.18.4)
Building wheels for collected packages: simpletraj
Building wheel for simpletraj (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: 'c:\users\mahmudk\appdata\local\programs\python\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\setup.py'"'"'; file='"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\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\mahmudk\AppData\Local\Temp\pip-wheel-5h50hx4k'
cwd: C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj
Complete output (51 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.5
creating build\lib.win-amd64-3.5\simpletraj
copying simpletraj\trajectory.py -> build\lib.win-amd64-3.5\simpletraj
copying simpletraj_init_.py -> build\lib.win-amd64-3.5\simpletraj
creating build\lib.win-amd64-3.5\simpletraj\dcd
copying simpletraj\dcd\dcd.py -> build\lib.win-amd64-3.5\simpletraj\dcd
copying simpletraj\dcd_init_.py -> build\lib.win-amd64-3.5\simpletraj\dcd
creating build\lib.win-amd64-3.5\simpletraj\xdrfile
copying simpletraj\xdrfile\libxdrfile2.py -> build\lib.win-amd64-3.5\simpletraj\xdrfile
copying simpletraj\xdrfile_init_.py -> build\lib.win-amd64-3.5\simpletraj\xdrfile
running build_ext
building 'simpletraj/xdrfile._libxdrfile2' extension
creating build\temp.win-amd64-3.5
creating build\temp.win-amd64-3.5\Release
creating build\temp.win-amd64-3.5\Release\simpletraj
creating build\temp.win-amd64-3.5\Release\simpletraj\xdrfile
C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Ic:\users\mahmudk\appdata\local\programs\python\python35\lib\site-packages\numpy\core\include -Ic:\users\mahmudk\appdata\local\programs\python\python35\include -Ic:\users\mahmudk\appdata\local\programs\python\python35\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /Tcsimpletraj/xdrfile/libxdrfile2_wrap.c /Fobuild\temp.win-amd64-3.5\Release\simpletraj/xdrfile/libxdrfile2_wrap.obj
libxdrfile2_wrap.c
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2061: syntax error: identifier 'xdr_tell'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2059: syntax error: ';'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2059: syntax error: ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2146: syntax error: missing ')' before identifier 'pos'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2061: syntax error: identifier 'pos'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ';'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ','
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ')'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2143: syntax error: missing ')' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2143: syntax error: missing '{' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2059: syntax error: ')'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2143: syntax error: missing ')' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2143: syntax error: missing '{' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2059: syntax error: ')'
c:\users\mahmudk\appdata\local\programs\python\python35\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
simpletraj/xdrfile/libxdrfile2_wrap.c(3108): error C2065: 'int64_t': undeclared identifier
simpletraj/xdrfile/libxdrfile2_wrap.c(3108): error C2297: '*': illegal, right operand has type 'int '
simpletraj/xdrfile/libxdrfile2_wrap.c(3110): warning C4013: 'read_xtc_numframes' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(3151): error C2065: 'int64_t': undeclared identifier
simpletraj/xdrfile/libxdrfile2_wrap.c(3151): error C2297: '': illegal, right operand has type 'int *'
simpletraj/xdrfile/libxdrfile2_wrap.c(3153): warning C4013: 'read_trr_numframes' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(3588): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data
simpletraj/xdrfile/libxdrfile2_wrap.c(3595): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data
simpletraj/xdrfile/libxdrfile2_wrap.c(4468): warning C4013: 'xdr_seek' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(4490): warning C4013: 'xdr_tell' undefined; assuming extern returning int
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe' failed with exit status 2

ERROR: Failed building wheel for simpletraj
Running setup.py clean for simpletraj
Failed to build simpletraj
Installing collected packages: simpletraj
Running setup.py install for simpletraj ... error
ERROR: Command errored out with exit status 1:
command: 'c:\users\mahmudk\appdata\local\programs\python\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\setup.py'"'"'; file='"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\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\mahmudk\AppData\Local\Temp\pip-record-zu_0pbwe\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\users\mahmudk\appdata\local\programs\python\python35\Include\simpletraj'
cwd: C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj
Complete output (51 lines):
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.5
creating build\lib.win-amd64-3.5\simpletraj
copying simpletraj\trajectory.py -> build\lib.win-amd64-3.5\simpletraj
copying simpletraj_init_.py -> build\lib.win-amd64-3.5\simpletraj
creating build\lib.win-amd64-3.5\simpletraj\dcd
copying simpletraj\dcd\dcd.py -> build\lib.win-amd64-3.5\simpletraj\dcd
copying simpletraj\dcd_init_.py -> build\lib.win-amd64-3.5\simpletraj\dcd
creating build\lib.win-amd64-3.5\simpletraj\xdrfile
copying simpletraj\xdrfile\libxdrfile2.py -> build\lib.win-amd64-3.5\simpletraj\xdrfile
copying simpletraj\xdrfile_init_.py -> build\lib.win-amd64-3.5\simpletraj\xdrfile
running build_ext
building 'simpletraj/xdrfile._libxdrfile2' extension
creating build\temp.win-amd64-3.5
creating build\temp.win-amd64-3.5\Release
creating build\temp.win-amd64-3.5\Release\simpletraj
creating build\temp.win-amd64-3.5\Release\simpletraj\xdrfile
C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Ic:\users\mahmudk\appdata\local\programs\python\python35\lib\site-packages\numpy\core\include -Ic:\users\mahmudk\appdata\local\programs\python\python35\include -Ic:\users\mahmudk\appdata\local\programs\python\python35\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /Tcsimpletraj/xdrfile/libxdrfile2_wrap.c /Fobuild\temp.win-amd64-3.5\Release\simpletraj/xdrfile/libxdrfile2_wrap.obj
libxdrfile2_wrap.c
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2061: syntax error: identifier 'xdr_tell'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2059: syntax error: ';'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(623): error C2059: syntax error: ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2146: syntax error: missing ')' before identifier 'pos'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2061: syntax error: identifier 'pos'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ';'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ','
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile.h(624): error C2059: syntax error: ')'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2143: syntax error: missing ')' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2143: syntax error: missing '{' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_trr.h(45): error C2059: syntax error: ')'
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2143: syntax error: missing ')' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2081: 'int64_t': name in formal parameter list illegal
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2143: syntax error: missing '{' before ''
C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\simpletraj\xdrfile\xdrfile_xtc.h(45): error C2059: syntax error: ')'
c:\users\mahmudk\appdata\local\programs\python\python35\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION simpletraj/xdrfile/libxdrfile2_wrap.c(3108): error C2065: 'int64_t': undeclared identifier
simpletraj/xdrfile/libxdrfile2_wrap.c(3108): error C2297: '*': illegal, right operand has type 'int '
simpletraj/xdrfile/libxdrfile2_wrap.c(3110): warning C4013: 'read_xtc_numframes' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(3151): error C2065: 'int64_t': undeclared identifier
simpletraj/xdrfile/libxdrfile2_wrap.c(3151): error C2297: '': illegal, right operand has type 'int *'
simpletraj/xdrfile/libxdrfile2_wrap.c(3153): warning C4013: 'read_trr_numframes' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(3588): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data
simpletraj/xdrfile/libxdrfile2_wrap.c(3595): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data
simpletraj/xdrfile/libxdrfile2_wrap.c(4468): warning C4013: 'xdr_seek' undefined; assuming extern returning int
simpletraj/xdrfile/libxdrfile2_wrap.c(4490): warning C4013: 'xdr_tell' undefined; assuming extern returning int
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Command errored out with exit status 1: 'c:\users\mahmudk\appdata\local\programs\python\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\setup.py'"'"'; file='"'"'C:\Users\mahmudk\AppData\Local\Temp\pip-install-6paxyeih\simpletraj\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\mahmudk\AppData\Local\Temp\pip-record-zu_0pbwe\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\users\mahmudk\appdata\local\programs\python\python35\Include\simpletraj' Check the logs for full command output.
@rena-96
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rena-96 commented Nov 12, 2020

Same problem. Did you find any solution to that?

@j0kaso
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j0kaso commented Nov 13, 2020

As far as I remember, we never tested it on Windows.
But it seems that the xdrfile from GROMACS is the issue. Maybe this helps? http://www.gromacs.org/Downloads/Installation_Instructions/Windows?highlight=comput

@rena-96
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rena-96 commented Nov 13, 2020

Thank you the the fast reply. I encountered problems with "simpletraj" installing the biobb packages (http://mmb.irbbarcelona.org/biobb/workflows/tutorials/md_setup). Now in the third line, I cannot create the environment because of simple tray. If I try to install it separately, I get the same output of the issue.
screen_simpletraj

@j0kaso
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j0kaso commented Nov 13, 2020

From the picture, it says that simpletraj package was not found, so you likely haven't installed it correctly.

I, unfortunately, can't help with installing simpletraj on Windows - I don't know if that's possible at all.

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@j0kaso @hasanmme @rena-96