rsgislib @2.1.20140825_3: build failure, update problems with Boost

[ForTozs]

I just wanted to report that rsgislib currently fails to build. I'm probably wasting space here, but this was the error:

:info:build [ 17%] Building CXX object src/CMakeFiles/rsgis_utils.dir/utils/RSGISPlotPolygonsCSVParse.cpp.o
:info:build cd /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/9135d61/src && /usr/bin/clang++  -Drsgis_utils_EXPORTS -I/opt/local -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/9135d61/src  -pipe -Os -stdlib=libc++ -Wall -Wpointer-arith -Wcast-align -Wcast-qual -Wredundant-decls -Wno-long-long -DNDEBUG -arch x86_64 -mmacosx-version-min=10.13 -fPIC   -o CMakeFiles/rsgis_utils.dir/utils/RSGISPlotPolygonsCSVParse.cpp.o -c /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/9135d61/src/utils/RSGISPlotPolygonsCSVParse.cpp
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/9135d61/src/utils/RSGISGEOSFactoryGenerator.cpp:34:27: error: calling a protected constructor of class 'geos::geom::GeometryFactory'
:info:build                 this->geomFactory = new geos::geom::GeometryFactory(this->pm);
:info:build                                         ^
:info:build /opt/local/include/geos/geom/GeometryFactory.h:453:2: note: declared protected here
:info:build         GeometryFactory(const PrecisionModel *pm);
:info:build         ^
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/9135d61/src/utils/RSGISGEOSFactoryGenerator.cpp:59:10: error: calling a protected destructor of class 'geos::geom::GeometryFactory'
:info:build                 delete geomFactory;
:info:build                        ^
:info:build /opt/local/include/geos/geom/GeometryFactory.h:474:10: note: declared protected here
:info:build         virtual ~GeometryFactory();

I'm trying to be more self-sufficient on MacPorts, so I tried to make my own patch. I directed the port to rsgislib version 3.4.9. With this I seem to be encountering some kind of problem with Boost, which seems to be a common problem recently, but I'm not sure how to fix the problem. My build failure happens at the very end (100%) and looks like this:

RSGISCmdHistoCube.cpp.o -Wl,-rpath,/opt/local/var/macports/build/_opt_local_var_macports_sources
_rsync.macports.org_release_tarballs_ports_gis_rsgislib/rsgislib/work/rsgislib-3.4.9/src librsgis_calib.1.1.0.dylib 
librsgis_classify.1.1.0.dylib librsgis_filter.1.0.0.dylib librsgis_modeling.1.1.0.dylib librsgis_radar.1.1.1.dylib 
librsgis_registration.1.2.0.dylib librsgis_segmentation.1.0.0.dylib librsgis_histocube.1.0.0.dylib -L/opt/local -
lboost_filesystem-mt -lboost_system-mt -lboost_date_time-mt -L/opt/local -lgdal -L/opt/local -lgsl -lgslcblas -
L/opt/local -lCGAL -L/opt/local -lgeos -L/opt/local -lmuparser -L/opt/local -lhdf5 -lhdf5_hl -lhdf5_cpp -L/opt/local -
lgmp -L/opt/local -lmpfr -L/opt/local -lkea -L/opt/local -lboost_filesystem-mt -lboost_system-mt -lboost_date_time-mt
 librsgis_vec.2.2.0.dylib librsgis_rastergis.2.0.0.dylib librsgis_img.3.0.0.dylib librsgis_geom.1.1.0.dylib 
librsgis_utils.1.1.0.dylib librsgis_maths.1.1.0.dylib librsgis_datastruct.1.1.0.dylib librsgis_commons.1.3.0.dylib -lgsl -
lgslcblas -lCGAL -lgeos -lmuparser -lkea -lxerces-c -L/opt/local -lboost_filesystem-mt -lboost_system-mt -
lboost_date_time-mt -lgdal -lhdf5 -lhdf5_hl -lhdf5_cpp -lgmp -lmpfr 

:info:build Undefined symbols for architecture x86_64:
:info:build   "boost::gregorian::greg_month::get_month_map_ptr()", referenced from:
:info:build       unsigned short boost::date_time::month_str_to_ushort<boost::gregorian::greg_month>
    (std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in 
    RSGISCmdHistoCube.cpp.o
:info:build ld: symbol(s) not found for architecture x86_64

I am not able to figure what is wrong here. It seems to be calling -lboost_date_time-mt, but is unable to link. This would be a great port to have up again, as py6S depends on it. It would also be valuable to me to see how this port is fixed. Thanks.

[ryandesign (Ryan Carsten Schmidt)]

Here's a patch that worked for me.

The patch does many things:

• Update to 3.4.9.
• Switch from cmake-1.0 to cmake-1.1 portgroup because all ports should do so.
• Add GitHub handle to maintainers line because all maintained ports should have that.
• Download from a tarball instead of the Mercurial repository because all ports that can should do that.
• Remove old patch which switched the Python install prefix. This is now controlled with a new cmake flag, so add -DINSTALL_PYTHON_USING_PREFIX=ON.
• cmake-1.1 defaults to building out of source, but this build system doesn't like that when building the Python module, so explicitly turn off out of source building.
• Convert reinplace that linked with multithreaded boost libraries if present into a patch that's always applied. We don't want ports to behave differently depending on what ports (or what variants of ports) are installed. And I don't think there's any variant of boost that causes it to build without the multithreaded libraries so it's fine to always use them.
• Remove reinplace that changed the documentation installation directory. The reinplace no longer changed anything in the CMakeLists.txt file, and I could not find any similar code there. It seems that no documentation is installed. I didn't look if it was still there somewhere.
• Alphabetize configure.args.
• Fix all the paths in configure.args.
• Remove -DCMAKE_VERBOSE_MAKEFILE=ON arg because the cmake portgroups already add that.
• Fix variant descriptions: Use imperative style, with capitalized first letter, and use actual Python version numbers.
• Remove unnecessary commented out code.

[ForTozs]

Thanks so much Ryan. It is extremely helpful to see what you did. Hopefully, I can do a better job fixing similar issues in the future and help give back to the community. Unfortunately, I am getting the same error (the second one) after cleaning and patching. This is helpful though. At least now I know it is likely specific to my system.

[ForTozs]

I managed to get it installed. Turns out my boost had the +gcc7 variant. I'm not sure if this is automatically selected when I have gcc7 selected with gcc_select, or if I had overlooked rebuilding with the default compiler. Setting:

sudo port select gcc mp-gcc5

and rebuilding boost/cgal/rsgislib fixed my issue. Thanks again.

EDIT: rsgislib will build fine with gcc set to gcc7, it just wouldn't build with the boost +gcc7 variant.

[ryandesign (Ryan Carsten Schmidt)]

Boost's gcc variants cause problems and need to be removed; see #55604.

[Veence (Vincent)]

I’m also bumping python variants to 35 and 36

[ForTozs]

Although it is installing fine, I'm not sure rsgislib is installing properly. If I call:

import rsgislib.imagecalc

I get:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/rsgislib/imagecalc/__init__.py", line 6, in <module>
    from ._imagecalc import *
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/rsgislib/imagecalc/_imagecalc.cpython-35m-darwin.so, \
2): Library not loaded: @rpath/librsgis_cmds.1.1.0.dylib
  Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/rsgislib/imagecalc/_imagecalc.cpython-35m-darwin.so
  Reason: image not found

I've tested on both Python 2.7 and 3.5, and I get the same result from both.

[ForTozs]

I'm new to all this, but I might have had a little luck (well, and Google). I am able to make the import after issuing the command:

sudo install_name_tool -add_rpath "/opt/local/lib" /opt/local/Library/Frameworks/
    Python.framework/Versions/3.5/lib/python3.5/site-packages/rsgislib/imagecalc/
    _imagecalc.cpython-35m-darwin.so

Now, this is likely not the preferred way, but I imagine I may be able to execute this with my Portfile with something like:

destroot {
    system "install_name_tool -add_rpath "/opt/local/lib" /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/rsgislib/imagecalc/_imagecalc.cpython-35m-darwin.so"
}

It is getting late over here and I won't be going any further tonight, but there are quite possibly many other rsgislib libraries that need to be linked properly. If anyone knows the best way to do this, please let me know.

[Veence (Vincent)]

Ok, you’re right, it fails on my computer too. I wrongly assumed Ryan had tested it besides the strict building phase. Thanks for the patch, I’m going to implement it not today, because no time, but tomorrow. Thanks also for your patience.

[ryandesign (Ryan Carsten Schmidt)]

Just so they get recorded in this ticket, Vincent's commits so far for this issue have been:

• [0af836f10f5733686f20cfa744f1cf05259f84a0/macports-ports]
• [fd078cb6ec5f68de9d652cce54e5b2e296609c5a/macports-ports]
• [60d0f2c9a1825776efc0b8e9ec6bac201c7ab63a/macports-ports]

What remains to be done?

[Veence (Vincent)]

I’m not sure this is relevant anymore. I’ll close it. Reopen if necessary.