Simpletraj installation problem

[hasanmme]

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]

Same problem. Did you find any solution to that?

[j0kaso]

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]

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.

[j0kaso]

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.