Dear PyMol Users, I am trying to install PyMol using Cygwin as described on the PyMol Wiki. I believe I have installed all the modules for cygwin that the Wiki said are required, however I am getting the following error message when trying to run the "python setup.py install" command in the Cygwin bash shell:
$ python setup.py install running install running build running build_py running build_ext building 'pymol._cmd' extension gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -DCYGWIN -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/python2.5 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.cygwin-1.7.5-i686-2.5/modules/cealign/src/ccealignmodule.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from modules/cealign/src/ccealignmodule.cpp:32: modules/cealign/src/ccealignmodule.H:38:21: error: jama_lu.h: No such file or directory modules/cealign/src/ccealignmodule.H:40:22: error: jama_svd.h: No such file or directory modules/cealign/src/ccealignmodule.cpp: In function 'PyObject* findBest(cePoint*, cePoint*, afp**, int, int, int)': modules/cealign/src/ccealignmodule.cpp:521: error: 'JAMA' has not been declared modules/cealign/src/ccealignmodule.cpp:521: error: expected primary-expression before 'double' modules/cealign/src/ccealignmodule.cpp:521: error: expected `;' before 'double' modules/cealign/src/ccealignmodule.cpp:532: error: 'svd' was not declared in this scope modules/cealign/src/ccealignmodule.cpp:543: error: 'JAMA' has not been declared modules/cealign/src/ccealignmodule.cpp:543: error: expected primary-expression before 'double' modules/cealign/src/ccealignmodule.cpp:543: error: expected `;' before 'double' modules/cealign/src/ccealignmodule.cpp:544: error: 'JAMA' has not been declared modules/cealign/src/ccealignmodule.cpp:544: error: expected primary-expression before 'double' modules/cealign/src/ccealignmodule.cpp:544: error: expected `;' before 'double' modules/cealign/src/ccealignmodule.cpp:546: error: 'LU_W' was not declared in this scope modules/cealign/src/ccealignmodule.cpp:546: error: 'LU_Vt' was not declared in this scope modules/cealign/src/ccealignmodule.cpp:553: warning: comparison between signed and unsigned integer expressions modules/cealign/src/ccealignmodule.cpp: In function 'TNT::Array2D<double> transpose(const TNT::Array2D<double>&)': modules/cealign/src/ccealignmodule.cpp:628: warning: comparison between signed and unsigned integer expressions modules/cealign/src/ccealignmodule.cpp:629: warning: comparison between signed and unsigned integer expressions error: command 'gcc' failed with exit status 1
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