Hi,
I also had problems compiling this last night. According to the following
(see "Compile and install" towards the bottom),
you have to call first:
export CPPFLAGS="-std=c++0x"
before doing the build call.
I used:
export CPPFLAGS="-std=c++11x"
so depends on your compiler.
HTH,
Tim
On Thu, Mar 19, 2015 at 11:38 AM, Matthew Baumgartner <mp...@pitt.edu>
wrote:
> Hi,
> I'm getting compile errors on the latest SVN build (4111).
> Any help would be appreciated.
>
> Thanks,
> Matt Baumgartner
>
> $ sudo python setup.py build -j 1
> fatal: Not a git repository (or any parent up to mount point /home)
> Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
> running build
> running build_py
> running build_ext
> building 'pymol._cmd' extension
> x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
> -O2 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE
> -D_PYMOL_OPENGL_SHADERS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE
> -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3
> -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
> -I/usr/local/lib/python2.7/dist-packages/numpy/core/include
> -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c
> layer0/Util.cpp -o build/temp.linux-x86_64-2.7/layer0/Util.o
> -Werror=implicit-function-declaration
> -Werror=declaration-after-statement -Wno-write-strings
> -Wno-unused-function -Wno-empty-body -Wno-char-subscripts -ffast-math
> -funroll-loops -O3 -fcommon
> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
> C/ObjC but not for C++ [enabled by default]
> x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
> -O2 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE
> -D_PYMOL_OPENGL_SHADERS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE
> -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3
> -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
> -I/usr/local/lib/python2.7/dist-packages/numpy/core/include
> -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c
> layer0/Crystal.cpp -o build/temp.linux-x86_64-2.7/layer0/Crystal.o
> -Werror=implicit-function-declaration
> -Werror=declaration-after-statement -Wno-write-strings
> -Wno-unused-function -Wno-empty-body -Wno-char-subscripts -ffast-math
> -funroll-loops -O3 -fcommon
> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
> C/ObjC but not for C++ [enabled by default]
> In file included from layer0/Crystal.cpp:30:0:
> layer1/PConv.h: In function ‘PyObject* PConvToPyObject(const
> std::set<T>&)’:
> layer1/PConv.h:236:8: warning: ‘auto’ changes meaning in C++11; please
> remove it [-Wc++0x-compat]
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:236:13: error: ‘it’ does not name a type
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:236:29: error: expected ‘;’ before ‘it’
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:236:29: error: ‘it’ was not declared in this scope
> layer1/PConv.h: In function ‘PyObject* PConvToPyObject(const std::map<K,
> V>&)’:
> layer1/PConv.h:253:8: warning: ‘auto’ changes meaning in C++11; please
> remove it [-Wc++0x-compat]
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:253:13: error: ‘it’ does not name a type
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:253:29: error: expected ‘;’ before ‘it’
> for (auto it = v.begin(); it != v.end(); ++it) {
> ^
> layer1/PConv.h:253:29: error: ‘it’ was not declared in this scope
> error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
