[PyMOL] pymol installation error
Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much of any help. Best regards.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] pymol installation error
Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much
Re: [PyMOL] pymol installation error
Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Dear all, > > Now I revised Line 4 in the SceneView.cpp file from > "#include " to > "#include ". > The error "layer1/SceneView.cpp:4:41: fatal error: > glm/ext/vector_relational.hpp: No such file or directory" > disappeared, but a now error appeared: > > layer1/SceneView.cpp:31:55: error: no matching function for call to > ‘equal(const vec3&, const vec3&, float)’ > Do you know how to deal with such an eorror? > > With many thanks! > Best regards > > -- > From:pymol-users > Send Time:2021年9月12日(星期日) 15:39 > To:pymol-users > Subject:[PyMOL] pymol installation error > > Dear pymol users, > > I am installing pymol in Centos 7 according to the guide in > https://pymolwiki.org/index.php/Linux_Install. I encounter an error of > "error: command 'g++' failed with exit status 1". A fill output of the > install command is as following: > > running build > running build_py > running build_ext > building 'pymol._cmd' extension > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > > g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat > -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE > -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC > -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include > -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include > -I/home/sunyp/software/anaconda/build/include > -I/home/sunyp/software/anaconda/build/include/freetype2 > -I/home/sunyp/software/anaconda/build/include/libxml2 > -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD > layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o > -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing > -Wno-char-subscripts -O3 -fopenmp > layer1/SceneView.cpp:4:41: > fatal error: glm/ext/vector_relational.hpp: No such file or directory > #include > ^ > compilation terminated. > > layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const > float*, int)’: > layer1/Scene.cpp:2557:42: > error: no matching function for call to ‘make_vec3(glm::vec3&)’ > > I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ > ^ > layer1/Sc
