search

schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
Other
1.2k stars 281 forks source link

Build fails with LTO due to ODR violations #395

Closed eli-schwartz closed 2 months ago

eli-schwartz commented 2 months ago

I tried to build with the following *FLAGS to optimize the build: -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing

Link-Time Optimization is a massively global compiler optimization pass which is pretty handy for producing faster executables. It also has the interesting property that because the compiler does whole-program analysis using bytecode, it can save type information and perform error checks that it normally doesn’t have enough insight for. In particular, checking for ODR issues and checking function type signature mismatches.

Note that all the -Werror=* flags are used to help detect cases where the compiler tries to optimize by assuming UB cannot exist in the source code -- if it does exist, ordinarily the code would be miscompiled, and this says to make the miscompilation a fatal error.

I got this error:

2024-09-04 17:32:02,648 root INFO x86_64-pc-linux-gnu-g++ -pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -std=c++17 -DNDEBUG -shared -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Werror=int-conversion -Werror=incompatible-pointer-types -DNDEBUG /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/build/generated/ShaderText.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/hash.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/inthash.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Bezier.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Block.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/CarveHelper.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/ContourSurf.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Crystal.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Err.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Feedback.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Field.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/File.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/GFXManager.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/GenericBuffer.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/GraphicsUtil.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Isosurf.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Map.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Match.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Matrix.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/MemoryDebug.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/MemoryUsage.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/MyPNG.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Parse.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Pixmap.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/PostProcess.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/ShaderMgr.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/ShaderPreprocessor.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/ShaderPrg.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Sphere.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/TTT.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Tetsurf.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Texture.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Tracker.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Triangle.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Util.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Util2.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Vector.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/Word.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/ccealignmodule.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/marching_cubes.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer0/os_gl.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Basis.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/ButMode.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/CGO.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/CGOGL.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/CGORenderer.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/COLLADA.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Camera.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Character.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Color.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Control.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Extrude.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Font.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUT.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUT8x13.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUT9x15.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUTHel10.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUTHel12.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontGLUTHel18.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/FontType.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Movie.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Ortho.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/P.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/PConv.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Picking.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Pop.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/PyMOLObject.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Ray.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Rep.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Scene.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SceneMouse.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/ScenePicking.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SceneRay.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SceneRender.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SceneView.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/ScrollBar.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Seq.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Setting.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Shaker.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SymOp.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SymOpPConv.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/SymOpTools.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Symmetry.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Text.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/TypeFace.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/View.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer1/Wizard.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/AssemblyHelpers.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/AtomInfo.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/AtomInfoHistory.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/BondTypeHistory.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/CifFile.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/CifMoleculeReader.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/CoordSet.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/DistSet.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/GadgetSet.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/HydrogenAdder.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/MmodTyping.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/MmtfMoleculeReader.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/Mol2Typing.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/MolV3000.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectAlignment.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectCGO.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectCallback.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectCurve.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectDist.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectGadget.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectGadgetRamp.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectGroup.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectMap.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectMesh.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectMolecule.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectMolecule2.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectMolecule3.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectSlice.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectSurface.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/ObjectVolume.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepAngle.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepCartoon.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepCylBond.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepDihedral.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepDistDash.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepDistLabel.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepDot.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepEllipsoid.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepLabel.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepMesh.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepNonbonded.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepNonbondedSphere.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepRibbon.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepSphere.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepSphereGenerate.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepSphereImmediate.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepSurface.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/RepWireBond.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/Sculpt.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/SculptCache.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/SideChainHelper.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer2/VFont.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/AtomIterators.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/CifDataValueFormatter.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/Editor.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/Executive.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/ExecutivePython.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/Interactions.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/MaeExportHelpers.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/MoleculeExporter.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/MovieScene.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/PlugIOManager.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/RingFinder.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/Seeker.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/Selector.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/SelectorTmp.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/SpecRec.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer3/SpecRecSpecial.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer4/Cmd.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer4/Menu.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer4/PopUp.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer5/PyMOL.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer5/TestPyMOL.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/layer5/main.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVContext.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVHeap.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVHeapArray.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVLexicon.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVOneToAny.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVOneToOne.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/OVRandom.o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/temp.linux-x86_64-cpython-312/ov/src/ov_utility.o -L/usr/lib64 -L/usr/lib -L/usr/lib64 -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -o /var/tmp/portage/sci-chemistry/pymol-3.0.0/work/pymol-open-source-3.0.0-python3_12/build/lib.linux-x86_64-cpython-312/pymol/_cmd.cpython-312-x86_64-linux-gnu.so -fopenmp
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:62:16: error: type ‘struct parm’ violates the C++ One Definition Rule [-Werror=odr]
   62 | typedef struct parm {
      |                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:59:16: note: a different type is defined in another translation unit
   59 | typedef struct parm {
      |                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:63:8: note: the first difference of corresponding definitions is field ‘title’
   63 |   char title[85];
      |        ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:60:17: note: a field with different name is defined in another translation unit
   60 |         char    ititl[81];
      |                 ^
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:33:3: error: type ‘struct parmdata’ violates the C++ One Definition Rule [-Werror=odr]
   33 | } parmdata;
      |   ^
contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:32:3: note: a different type is defined in another translation unit
   32 | } parmdata;
      |   ^
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:28:15: note: the first difference of corresponding definitions is field ‘prm’
   28 |   parmstruct *prm;
      |               ^
contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:28:13: note: a field with different name is defined in another translation unit
   28 |   ReadPARM *rp;
      |             ^
layer0/Isosurf.cpp:47:16: error: type ‘struct PointType’ violates the C++ One Definition Rule [-Werror=odr]
   47 | typedef struct PointType {
      |                ^
layer0/Tetsurf.cpp:46:3: note: a different type is defined in another translation unit
   46 | } PointType;
      |   ^
layer0/Isosurf.cpp:49:7: note: the first difference of corresponding definitions is field ‘NLink’
   49 |   int NLink;
      |       ^
layer0/Tetsurf.cpp:43:9: note: a field with different name is defined in another translation unit
   43 |   float Normal[3];
      |         ^
ov/src/OVOneToAny.cpp:15:3: error: type ‘struct up_element’ violates the C++ One Definition Rule [-Werror=odr]
   15 | } up_element;
      |   ^
ov/src/OVOneToOne.cpp:15:3: note: a different type is defined in another translation unit
   15 | } up_element;
      |   ^
ov/src/OVOneToOne.cpp:14:25: note: the first difference of corresponding definitions is field ‘reverse_next’
   14 |   ov_size forward_next, reverse_next;
      |                         ^
ov/src/OVOneToOne.cpp:15:3: note: a type with different number of fields is defined in another translation unit
   15 | } up_element;
      |   ^
lto1: some warnings being treated as errors
lto-wrapper: fatal error: /usr/bin/x86_64-pc-linux-gnu-g++ returned 1 exit status
compilation terminated.
/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
error: command '/usr/bin/x86_64-pc-linux-gnu-g++' failed with exit code 1
 * ERROR: sci-chemistry/pymol-3.0.0::gentoo failed (compile phase):

Originally reported downstream: https://bugs.gentoo.org/933235 Full build log: build.log

eli-schwartz commented 2 months ago

From a quick look, e.g. parm vs parm7 define similar types using the same name.

JarrettSJohnson commented 2 months ago

Thanks for the report. Should be resolved now.

eli-schwartz commented 2 months ago

Thank you for the fast response! :)

(I have not tested the change as the approach to building the package seems to have changed quite a bit in git master, so I'm going to wait until the maintainer of the distro package upgrades to the next version.)