pymol: error: no type named 'shared_ptr' in namespace 'std'

[kathryncole]

I am unable to install Pymol. I upgraded my MacPorts, did sudo install, and sudo clean, but I am getting the following error:

Error: org.macports.destroot for port pymol returned: command execution failed
Please see the log file for port pymol for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/main.log

I searched the previous tickets, and see that there have been similar reports, but I am unsure of the best/ most current solution. Thank you for your help!

[kathryncole]

main.log

[ryandesign (Ryan Carsten Schmidt)]

The error in the log is:

error: no type named 'shared_ptr' in namespace 'std'

I think this error means the port requires C++11.

The log also shows this is on OS X 10.8, which uses libstdc++ by default which does not support C++11.

The current MacPorts solution to this type of problem is to include the cxx11 portgroup by writing:

PortGroup cxx11 1.0

after the PortSystem line in the portfile. This will cause the user to be directed to a web page that informs them how they can resolve the problem.

[howarth.at.macports@…]

This change seems to have been introduced in ​http://sourceforge.net/p/pymol/code/4133/tree//trunk/pymol/layer2/ObjectMolecule.h?diff=50c0fc56e88f3d0bdf694277:4132 so a bug report should be filed upstream.

[howarth.at.macports@…]

Filed ​https://sourceforge.net/p/pymol/bugs/171/ to report this upstream.

[howarth.at.macports@…]

Can someone on 10.7 or 10.8 test the attached Portfile.diff and associated osx108-no-cxx11.patch?

[howarth.at.macports@…]

patch to avoid unsupported c++11 code on 10.8 or earlier

[howarth.at.macports@…]

The proposed fix ix incomplete as the build on 10.7 with Xcode 4.6's clang still fails with...

: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.

[howarth.at.macports@…]

Using libc++ isn't a viable option prior to OS X 10.9. The initial libc++ support was only introduced in OS X 10.7 and the c++-11 support was not fully complete until the OS X 10.9 when Apple switched the system default c++ library. So you really can't depend on all of the features and functionality of c++-11 being present in the libc++ of 10.7/10.8. Unlike FreeBSD, OS X has no libcxxrt shim library (​https://wiki.freebsd.org/NewC++Stack) to attempt to bridge the ABI differences in the two c++ libraries. This is why you will find that fink, MacPorts, etc all build their open source packages with libstdc++ up to OS X 10.8 and then completed switched over to libc++ starting with OS X 10.9.

[howarth.at.macports@…]

Upstream is recommending that we build pymol svn with -stdlib=libc++ passed on CXXFLAGS on 10.7/10.8 (which means that 10.6 and earlier won't be able to build pymol unless we use la recent lvm.org clang/libc++). This happens to work at the moment because 1) python isn't built against c++ so there is no ABI issues and 2) pymol currently doesn't directly link to any code built with c++. IMHO, this is a bit fragile in the long run but will work for now on 10.7/10.8. The approach could potentially break later if upstream keeps expanding the usage of c++-11 features and eventually runs into missing c++-11 support in the early system libc++ of 10.7/10.8.

[kathryncole]

I just tried:

sudo port install pymol -stdlib=libc++

which failed, so I ran sudo port clean pymol and tried the above command again, but received the following error:

Error: org.macports.destroot for port pymol returned: command execution failed

I attached the log file.

[kathryncole]

-stdlib=libc++ main.log

[howarth.at.macports@…]

The attached Portfile.diff adds -stdlib=libc++ when the clang compilers are in use. It also drops support for FSF gcc variants prior to gcc 4.7 to insure that those variants have c++-11 support going forward.

[howarth.at.macports@…]

The attached Portfile.diff and pymol_no_cxx11.patch patch is the upstream fix to properly address this problem so that older OS X releases (prior to 10.9) can continue to build against libstdc++. Tested on 10.7 and 10.11.

[howarth.at.macports@…]

Portfile diff to properly address c++11 issue for older OS X releases using upstream patch

[howarth.at.macports@…]

Upstream fix to properly address lack of c++11 support in legacy libstdc++ of earlier OS X

[howarth.at.macports@…]

Opened a new ticket...

#49666

...to update pymol to svn r4041 in order to obtain the committed fix...

r4141 | speleo3 | 2015-11-11 19:10:37 -0500 (Wed, 11 Nov 2015) | 2 lines

backport to pre-c++11 for OS X <= 10.8

[ryandesign (Ryan Carsten Schmidt)]

The patch to setup.py seems to base its decision on whether to use C++11 features on whether the OS X version is 10.9 or greater. This is not necessarily correct; it is possible to use libc++ on older systems which will give them C++11 support so you should find a more accurate way to determine if C++11 support is available.

I assume the patch you've attached here has been included in the upstream repository and is superseded by the update in #49666 so I committed that instead of this in r142439.