Summary: | [science overlay] sci-chemistry/avogadro-1.1.0 - ld: spglib/libspglib.a(spglib.c.o): warning: relocation in readonly section `.text'. | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | rei4dan |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
See Also: | https://bugs.gentoo.org/show_bug.cgi?id=439436 | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | 439436 | ||
Bug Blocks: | |||
Attachments: | /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log |
Description
Juergen Rose
2012-10-23 15:23:04 UTC
Created attachment 327230 [details]
/var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log
I can't reproduce it. Could it be gcc or cmake issue? Note that I'm using ~amd64. I tried with gcc-4.6.3 and 4.7.2 and both compiled it without any such errors. Linking CXX shared module ../../../../lib64/crystallographyextension.so cd /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography && /usr/bin/cmake -E cmake_link_ script CMakeFiles/crystallographyextension.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-g++ -fPIC -march=native -mtune=native -O3 -pipe -ggdb -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,crystallographyextension.so -o ../../../../lib64/crystallographyextension.so CMakeFiles/crystallographyextension.dir/avospglib.cpp.o CMakeFiles/crystallographyextension.dir/ceundo.cpp.o CMakeFiles/crystallographyextension.dir/crystallographyextension.cpp.o CMakeFiles/crystallographyextension.dir/crystalpastedialog.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceabstractdockwidget.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceabstracteditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/cecoordinateeditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/cematrixeditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceparametereditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceslabbuilder.cpp.o CMakeFiles/crystallographyextension.dir/ui/cetranslatewidget.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceviewoptionswidget.cpp.o CMakeFiles/crystallographyextension.dir/moc_crystallographyextension.cxx.o CMakeFiles/crystallographyextension.dir/moc_crystalpastedialog.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceabstractdockwidget.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceabstracteditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cecoordinateeditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cematrixeditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceparametereditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceslabbuilder.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cetranslatewidget.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceviewoptionswidget.cxx.o ../../../../lib64/libavogadro.so.1.1.0 /usr/lib64/qt4/libQtCore.so /usr/lib64/qt4/libQtGui.so -lopenbabel -lGLU -lGL -lSM -lICE -lX11 -lXext spglib/libspglib.a -Wl,-rpath,/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/lib 64:/usr/lib64/qt4: Also scanelf doesn't report any text relocations in libspglib.a: # scanelf -tmyA /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a TYPE TEXTREL FILE ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:cell.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:debug.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:hall_symbol.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:lattice.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:mathfunc.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:pointgroup.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:primitive.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:refinement.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spacegroup.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spg_database.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spglib.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:symmetry.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:symmetry_kpoint.c.o I would think it is a x86 problem like Jürgens emerge --info says. Perhaps we should go upstream with this. Pleas make your build log verbose and resubmit it. This is how the object in question is built on my system: [ 4%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-lin ux-gnu-gcc -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_PLUGIN -DQT_SHARED -DND EBUG -march=native -mtune=native -O3 -pipe -ggdb -fPIC -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work /avogadro-1.1.0_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include/boost-1_49 -I/usr/include/python2.7 -I/var/tmp /portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogad ro-1.1.0/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystal lography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0/libavogadro/src/extensions/crystallography -w -o CMakeFiles/spglib.dir /spglib.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0/libavogadro/src/extensions/crystallography/spglib/spglib.c /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/CMakeFiles Yes, it might be -fPIC issue or something for x86. I'll ping upstream. How can I make my build log more verbose? (In reply to comment #8) > How can I make my build log more verbose? CMAKE_VERBOSE=1 Hi Justin, how should I apply CMAKE_VERBOSE=1? I tried "CMAKE_VERBOSE=1 emerge -uvDN avogadro", but the log file seems to be shorter than before: root@tiger:/root(6)# ll /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log -rw-rw---- 1 portage portage 711693 Nov 13 13:52 /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log Please try CMAKE_VERBOSE="true" Now I did 'CMAKE_VERBOSE="true" emerge -uvDN avogadro', but there seems to be no essential change in /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log: root@tiger:/root(10)# ll /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log -rw-rw---- 1 portage portage 711693 Nov 13 16:02 /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log Oh I am really sorry, you build log is already verbose. Sorry for that. 06 Dec 2012; Justin Lecher <jlec@gentoo.org> avogadro-1.1.0.ebuild, + +files/avogadro-1.1.0-textrel.patch: + Add patch to avoid textrels on i686, #439410 + |