| Summary: | sci-libs/vtk-6.1.0-r1 linker error | ||
|---|---|---|---|
| Product: | Gentoo/Alt | Reporter: | Jeffrey Ratcliffe <Jeffrey.Ratcliffe> |
| Component: | Prefix Support | Assignee: | Gentoo Prefix <prefix> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
The symbol is defined in the qt in prefix, so I assume that for some reason, the libraries in this directory are not being searched in this case: $ scanelf -s _ZNK19QAbstractProxyModel8itemDataERK11QModelIndex /home/jeff/gentoo/usr/lib/qt4/ TYPE SYM FILE ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtCore.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtXml.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtNetwork.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtScript.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtSql.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtXmlPatterns.so.4.8.7 ET_DYN _ZNK19QAbstractProxyModel8itemDataERK11QModelIndex /home/jeff/gentoo/usr/lib/qt4/libQtScriptTools.so.4.8.7 ET_DYN _ZNK19QAbstractProxyModel8itemDataERK11QModelIndex /home/jeff/gentoo/usr/lib/qt4/libQtGui.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtSvg.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtOpenGL.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtDeclarative.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtWebKit.so.4.10.4 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtDesignerComponents.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtDesigner.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtHelp.so.4.8.7 ET_DYN - /home/jeff/gentoo/usr/lib/qt4/libQtCLucene.so.4.8.7 Interestingly running strace python -c "import vtk", it does go looking for the correctly library, but not in the right place:
open("/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/usr/lib/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/lib/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY) = 6
fstat(6, {st_mode=S_IFREG|0644, st_size=154450, ...}) = 0
mmap(NULL, 154450, PROT_READ, MAP_PRIVATE, 6, 0) = 0x2acdf7e58000
close(6) = 0
open("/usr/lib64/qt4/lib64/libQtGui.so.4", O_RDONLY) = 6
With a basic PyQt4 program, it finds the library:
open("/home/jeff/gentoo/usr/lib/qt4/tls/x86_64/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/home/jeff/gentoo/usr/lib/qt4/tls/x86_64", 0x7fff3a41f4d0) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/usr/lib/qt4/tls/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/home/jeff/gentoo/usr/lib/qt4/tls", 0x7fff3a41f4d0) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/usr/lib/qt4/x86_64/libQtGui.so.4", O_RDONLY) = -1 ENOENT (No such file or directory)
stat("/home/jeff/gentoo/usr/lib/qt4/x86_64", 0x7fff3a41f4d0) = -1 ENOENT (No such file or directory)
open("/home/jeff/gentoo/usr/lib/qt4/libQtGui.so.4", O_RDONLY) = 4
can you please try re-emerging binutils-config-5 and re-emerging vtk? Thanks for the help. I re-emerged binutils-config and then gcc-config for good measure. vtk then wouldn't even emerge, stopping right at the beginning of configure, looking for symbols in from libstdc++.so.6 and not finding them in the host. I then re-emerged gcc (which took me coincidently from 4.8.4->4.8.5). I was then able to re-emerge vtk, but still cannot import vtk from python, failing with the same error as before. what does scanelf --rpath /home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 return? $ scanelf --rpath /home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 TYPE RPATH FILE ET_DYN /home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/usr/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/lib /home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 ok, so it's built wrong, because it doesn't include the rpath entry to where the qt lib it needs is supposed to be From my understanding, the libraries are first built, then stripped, then copied to the image directory before they are merged. From what I can tell, the qt directory is in the path after being built and stripped, but not in the image: $ scanelf --rpath /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib/libvtkGUISupportQt.so.1 /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib/libvtkGUISupportQt.so.1-stripped /scratch/portage/sci-libs/vtk-6.1.0-r2/image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 TYPE RPATH FILE ET_DYN /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib:/home/jeff/gentoo/usr/lib/qt4:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/usr/lib:/home/jeff/gentoo/lib::/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/lib /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib/libvtkGUISupportQt.so.1 ET_DYN /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib:/home/jeff/gentoo/usr/lib/qt4:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/usr/lib:/home/jeff/gentoo/lib::/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/lib /scratch/portage/sci-libs/vtk-6.1.0-r2/work/vtk-6.1.0_build/lib/libvtkGUISupportQt.so.1-stripped ET_DYN /home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/usr/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib/gcc:/home/jeff/gentoo/usr/x86_64-pc-linux-gnu/lib:/home/jeff/gentoo/lib:/home/jeff/gentoo/usr/lib /scratch/portage/sci-libs/vtk-6.1.0-r2/image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 That made me look in the cmake-utils.eclass - which indeed does not include the path to the qt4 libraries:
SET(CMAKE_INSTALL_RPATH "${EPREFIX}${PREFIX}/lib;${EPREFIX}/usr/${CHOST}/lib/gcc;${EPREFIX}/usr/${CHOST}/lib;${EPREFIX}/usr/$(get_libdir);${EPREFIX}/$(get_libdir)" CACHE STRING "" FORCE)
So I hacked the ebuild to add the qt4 path to the cmake before cmake-utils_src_install:
sed -i "s!${EPREFIX}/usr/$(get_libdir);!${EPREFIX}/usr/$(get_libdir);${EPREFIX}/usr/$(get_libdir)/qt4;!" "${BUILD_DIR}"/gentoo_rules.cmake || die
This is a horrible, horrible hack, but python -c "import vtk" now works.
What would be a less hacky solution?
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4dd17f5b702e2f5fd47c9ddf33bd306b1a8dffab commit 4dd17f5b702e2f5fd47c9ddf33bd306b1a8dffab Author: Andreas Sturmlechner <asturm@gentoo.org> AuthorDate: 2019-12-28 16:05:59 +0000 Commit: Andreas Sturmlechner <asturm@gentoo.org> CommitDate: 2019-12-28 16:09:54 +0000 sci-libs/vtkdata: Remove last-rited package Closes: https://bugs.gentoo.org/542756 Closes: https://bugs.gentoo.org/554388 Closes: https://bugs.gentoo.org/555768 Closes: https://bugs.gentoo.org/557974 Closes: https://bugs.gentoo.org/574854 Closes: https://bugs.gentoo.org/574890 Closes: https://bugs.gentoo.org/589182 Closes: https://bugs.gentoo.org/590640 Closes: https://bugs.gentoo.org/612302 Closes: https://bugs.gentoo.org/622574 Closes: https://bugs.gentoo.org/698940 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> profiles/package.mask | 7 ------- sci-libs/vtkdata/Manifest | 1 - sci-libs/vtkdata/metadata.xml | 8 -------- sci-libs/vtkdata/vtkdata-6.1.0.ebuild | 26 -------------------------- 4 files changed, 42 deletions(-) |
sci-libs/vtk-6.1.0-r1 emerges without problem. However: $ python Python 2.7.11 (default, Feb 5 2016, 12:57:24) [GCC 4.8.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import vtk Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/jeff/gentoo/usr/lib/python2.7/site-packages/vtk/__init__.py", line 115, in <module> from vtkRenderingQt import * File "/home/jeff/gentoo/usr/lib/python2.7/site-packages/vtk/vtkRenderingQt.py", line 1, in <module> from vtkRenderingQtPython import * ImportError: /home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1: undefined symbol: _ZNK19QAbstractProxyModel8itemDataERK11QModelIndex Reproducible: Always Indeed: $ ldd -r ../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1 | grep lib64 ../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1: /usr/lib64/libz.so.1: no version information available (required by /home/jeff/gentoo/usr/lib/libpng16.so.16) libQtGui.so.4 => /usr/lib64/qt4/lib64/libQtGui.so.4 (0x00002af93bf32000) libQtNetwork.so.4 => /usr/lib64/qt4/lib64/libQtNetwork.so.4 (0x00002af93c834000) libQtCore.so.4 => /usr/lib64/qt4/lib64/libQtCore.so.4 (0x00002af93ca92000) libm.so.6 => /lib64/libm.so.6 (0x00002af9412a0000) libc.so.6 => /lib64/libc.so.6 (0x00002af941523000) libdl.so.2 => /lib64/libdl.so.2 (0x00002af9426fd000) libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002af942902000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002af942b26000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002af942d3a000) libXi.so.6 => /usr/lib64/libXi.so.6 (0x00002af942f56000) libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00002af94315f000) libXrandr.so.2 => /usr/lib64/libXrandr.so.2 (0x00002af943368000) libXcursor.so.1 => /usr/lib64/libXcursor.so.1 (0x00002af94356b000) libXinerama.so.1 => /usr/lib64/libXinerama.so.1 (0x00002af943776000) libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00002af943978000) libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00002af943bfc000) /lib64/ld-linux-x86-64.so.2 (0x0000003c53a00000) libexpat.so.0 => /lib64/libexpat.so.0 (0x00002af947322000) librt.so.1 => /lib64/librt.so.1 (0x00002af947950000) symbol inflateReset2, version ZLIB_1.2.3.4 not defined in file libz.so.1 with link time reference (/home/jeff/gentoo/usr/lib/libpng16.so.16) undefined symbol: _ZNK19QAbstractProxyModel8itemDataERK11QModelIndex (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN19QAbstractProxyModel11setItemDataERK11QModelIndexRK4QMapIi8QVariantE (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZNK18QStandardItemModel9mimeTypesEv (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZNK18QStandardItemModel8mimeDataERK5QListI11QModelIndexE (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN18QStandardItemModel12dropMimeDataEPK9QMimeDataN2Qt10DropActionEiiRK11QModelIndex (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN11QVectorData10reallocateEPS_iii (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN18QAbstractItemModel13endResetModelEv (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN9QHashData12allocateNodeEi (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN9QListData11detach_growEPii (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN9QHashData11free_helperEPFvPNS_4NodeEE (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN9QListData6detachEi (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN18QAbstractItemModel15beginResetModelEv (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN9QHashData14detach_helper2EPFvPNS_4NodeEPvEPFvS1_Eii (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN11QVectorData4freeEPS_i (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN8QPainter9drawImageERK7QPointFRK6QImage (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _Z9qBadAllocv (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN8QVariantC1EiPKvj (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) undefined symbol: _ZN11QVectorData8allocateEii (../../image/home/jeff/gentoo/usr/lib/libvtkGUISupportQt.so.1) However, if I look at the library before it is installed: $ ldd -r lib/libvtkGUISupportQt.so.1 | grep lib64 libm.so.6 => /lib64/libm.so.6 (0x00002b67e4754000) libc.so.6 => /lib64/libc.so.6 (0x00002b67e49d7000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b67e5bb1000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b67e5db6000) librt.so.1 => /lib64/librt.so.1 (0x00002b67e61d4000) /lib64/ld-linux-x86-64.so.2 (0x0000003c53a00000) But stripping itself is not the problem: $ x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line -R .note.gnu.gold-version lib/libvtkGUISupportQt.so.1 -o lib/libvtkGUISupportQt.so.1-stripped $ ldd -r lib/libvtkGUISupportQt.so.1 | grep lib64 libm.so.6 => /lib64/libm.so.6 (0x00002b1303d10000) libc.so.6 => /lib64/libc.so.6 (0x00002b1303f93000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b130516d000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b1305372000) librt.so.1 => /lib64/librt.so.1 (0x00002b1305790000) /lib64/ld-linux-x86-64.so.2 (0x0000003c53a00000) $ ldd -r lib/libvtkGUISupportQt.so.1-stripped | grep lib64 libm.so.6 => /lib64/libm.so.6 (0x00002b3554e7c000) libc.so.6 => /lib64/libc.so.6 (0x00002b35550ff000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b35562d9000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b35564de000) librt.so.1 => /lib64/librt.so.1 (0x00002b35568fc000) /lib64/ld-linux-x86-64.so.2 (0x0000003c53a00000) Any pointers would be most welcome.