#171 r 4133 breaks pymol builds on legacy system libstdc++ of OS X <= 10.8

[Jack Howarth]

Starting with...

https://sourceforge.net/p/pymol/code/4133/tree/trunk/pymol/layer2/ObjectMolecule.h?diff=50c0fc56e88f3d0bdf694277:4132

pymol svn is c++11-centric and no longer builds on OS X against their legacy libstdc++ library....

https://trac.macports.org/ticket/49449#comment:1

https://trac.macports.org/attachment/ticket/49449/main.log

Was this change intentional?

[Thomas Holder]

compatibility with old compilers is not high priority, but will be considered if feasable. What is __cplusplus set to on your system?

[Thomas Holder]

please try the attached patch
(disables the optional feature http://pymolwiki.org/index.php/cif_keepinmemory)

[Jack Howarth]

The proposed patch is incomplete for restoring the legacy libstdc++ build. Testing on 10.7 against Apple clang from Xcode 4.6 fails with...

:info:destroot /usr/bin/clang++ -std=c++0x -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NO_CXX11 -D_P
YMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plu
gins/molfile_plugin/src -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/opt/local/include -I/opt/lo
cal/include/freetype2 -I/opt/local/include/libxml2 -I/usr/include -I/usr/include/libxml2 -I/usr/X11/include -I/usr/X11/include/freetype2 -I/opt/local/Library/Frame
works/Python.framework/Versions/2.7/include/python2.7 -c layer2/AtomInfo.cpp -o build/temp.macosx-10.7-x86_64-2.7/layer2/AtomInfo.o -Wno-narrowing -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 -g -fcommon
:info:destroot layer2/AtomInfo.cpp:1166:12: error: no member named 'copy_n' in namespace 'std'; did you mean 'copy'?
:info:destroot       std::copy_n(u, 6, I->get_anisou());
:info:destroot       ~~~~~^~~~~~
:info:destroot            copy
:info:destroot /usr/include/c++/4.2.1/bits/stl_algobase.h:389:5: note: 'copy' declared here
:info:destroot     copy(_InputIterator __first, _InputIterator __last,
:info:destroot     ^
:info:destroot layer2/AtomInfo.cpp:1166:7: error: no matching function for call to 'copy'
:info:destroot       std::copy_n(u, 6, I->get_anisou());
:info:destroot       ^~~~~~~~~~~
:info:destroot /usr/include/c++/4.2.1/bits/stl_algobase.h:389:5: note: candidate template ignored: deduced conflicting types for parameter '_InputIterator' ('float
 *' vs. 'int')
:info:destroot     copy(_InputIterator __first, _InputIterator __last,
:info:destroot     ^
:info:destroot layer2/AtomInfo.cpp:1199:10: error: no member named 'copy_n' in namespace 'std'layer1/CGO.cpp:; did you mean8535: 'copy'?
:info:destroot     std::copy_n(src->anisou, 6, dst->get_anisou());
:info:destroot     ~~~~~^~~~~~
:info:destroot          copy
:info:destroot /usr/include/c++/4.2.1/bits/stl_algobase.h:389:5: note: 'copy' declared here
:info:destroot     copy(_InputIterator __first, _InputIterator __last,
:info:destroot 5: warning: expression result unused    ^
:info:destroot layer2/AtomInfo.cpp:1199:5: error: no matching function for call to 'copy'
:info:destroot     std::copy_n(src->anisou, 6, dst->get_anisou());
:info:destroot     ^~~~~~~~~~~
:info:destroot /usr/include/c++/4.2.1/bits/stl_algobase.h:389:5: note: candidate template ignored: deduced conflicting types for parameter '_InputIterator' ('float
 *' vs. 'int')
:info:destroot     copy(_InputIterator __first, _InputIterator __last,
:info:destroot     ^
:info:destroot  [-Wunused-value]
:info:destroot     CGO_read_int(pc);
:info:destroot     ^~~~~~~~~~~~~~~~
:info:destroot layer1/CGO.h:34:26: note: expanded from macro 'CGO_read_int'
:info:destroot #define CGO_read_int(p) (*((int*)((p)++)))
:info:destroot                          ^~~~~~~~~~~~~~~~
:info:destroot 4 errors generated.

[Thomas Holder]

have you tried
export CXXFLAGS="-stdlib=libc++"

[Jack Howarth]

Using...

export CXXFLAGS="-stdlib=libc++"

isn't appropriate prior to OS X 10.9 as the libc++ present in 10.7/10.8 lacks complete c++-11 support.

[Thomas Holder]

I successfully compiled pymol on OS X 10.7.5 with /usr/bin/python2.7, using /usr/bin/clang++ and CXXFLAGS="-stdlib=libc++"

No modification on the C++11 code. I had to modify the files "monkeypatch_distutils.py" and "setup.py" and do some trickery to force distutils to use clang++ instead of llvm-g++-4.2

[Jack Howarth]

This approach only works because pymol currently doesn't link against any additional c++-based support libraries. While some of the current dependencies like scipy currently build as c++, that code is isolated into its own python modules so there is no mixing of the two c++ libraries. See...

https://wiki.freebsd.org/NewC++Stack

on the issues with mixing the two c++ ABI's.

[Thomas Holder]

thanks for clarifying.

Backport patch applied to SVN 4141.