Summary: | [science overlay] sci-chemistry/modeller-9.12: is permanently reemerged by revdep-rebuild because libmodeller.so.8 is not found | ||
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Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED WONTFIX | ||
Severity: | normal | CC: | andrewammerlaan |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: | The output of revdep-rebuild -vvvp |
Description
Juergen Rose
2013-06-25 08:48:19 UTC
+ 26 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r1.ebuild, + +modeller-9.12-r2.ebuild: + Fix lib position, #474696 + The issue happens now again with sci-chemistry/modeller-9.12-r2 and 'emerge @preserved-rebuild'. 'emerge @preserved-rebuild' emerges modeller over and over again; root@leopard:/root(2)# emerge @preserved-rebuild Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 3) sci-chemistry/modeller-9.12-r2 from science * modeller-9.12.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking modeller-9.12.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... * QA warning: python_prepare_all() didn't call distutils-r1_python_prepare_all >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... * python2_7: running distutils-r1_run_phase python_compile /usr/bin/python2.7 setup.py build --build-base /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12-python2_7 --build-platlib /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12-python2_7/lib --build-purelib /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12-python2_7/lib --build-scripts /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12-python2_7/scripts running build running build_ext building '_modeller' extension ... >>> Installing (1 of 3) sci-chemistry/modeller-9.12-r2 * This package leaves a license Key file in /opt/modeller/modlib/modeller/config.py * that you need to remove to completely get rid of modeller. * Obtain a license Key from * http://salilab.org/modeller/registration.html * And run this before using modeller: * emerge --config =sci-chemistry/modeller-9.12-r2 * That way you can [re]enter your license key. >>> Emerging (2 of 3) media-gfx/freecad-0.12.5284-r3 ... >>> Failed to emerge media-gfx/freecad-0.12.5284-r3, Log file: >>> '/var/tmp/portage/media-gfx/freecad-0.12.5284-r3/temp/build.log' * GNU info directory index is up-to-date. !!! existing preserved libs: >>> package: media-libs/libjpeg-turbo-1.3.0-r2 * - /usr/lib64/libjpeg.so.8 * - /usr/lib64/libjpeg.so.8.0.2 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: sci-libs/hdf5-1.8.11 * - /usr/lib64/libhdf5.so.7 * - /usr/lib64/libhdf5.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.7 (sci-chemistry/modeller-9.12-r2) * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r2) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) * - /usr/lib64/libhdf5_hl.so.7 * - /usr/lib64/libhdf5_hl.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r2) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: dev-libs/boost-1.53.0 root@leopard:/root(3)# emerge @preserved-rebuild Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 3) sci-chemistry/modeller-9.12-r2 from science * modeller-9.12.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking modeller-9.12.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... * QA warning: python_prepare_all() didn't call distutils-r1_python_prepare_all >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12 ... * python2_7: running distutils-r1_run_phase python_compile /usr/bin/python2.7 setup.py build --build-base /var/tmp/portage/sci-chemistry/modeller-9.12-r2/work/modeller-9.12-python2_7 --build ... + 20 Sep 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r2.ebuild, + +modeller-9.12-r3.ebuild: + Mask lib dir for revdep-rebuild, #474696 + Still the same issue with 'emerge @preserved-rebuild' and gentoolkit-0.3.0.8-r2 and portage-2.2.7. What is the ourput of revdep-rebuild -vvvp ? Created attachment 361096 [details]
The output of revdep-rebuild -vvvp
(In reply to Juergen Rose from comment #6) > Created attachment 361096 [details] > The output of revdep-rebuild -vvvp Does this mean everything is fixed now? (In reply to Justin Lecher from comment #7) > (In reply to Juergen Rose from comment #6) > > Created attachment 361096 [details] > > The output of revdep-rebuild -vvvp > > Does this mean everything is fixed now? No, it is not fixed: !!! existing preserved libs: >>> package: media-video/ffmpeg-1.2.4 * - /usr/lib64/libavutil.so.51 * - /usr/lib64/libavutil.so.51.73.101 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: media-libs/libjpeg-turbo-1.3.0-r2 * - /usr/lib64/libjpeg.so.8 * - /usr/lib64/libjpeg.so.8.0.2 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: sci-libs/hdf5-1.8.11 * - /usr/lib64/libhdf5.so.7 * - /usr/lib64/libhdf5.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.7 (sci-chemistry/modeller-9.12-r3) * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) * - /usr/lib64/libhdf5_hl.so.7 * - /usr/lib64/libhdf5_hl.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: dev-libs/boost-1.53.0 ... root@leopard:/root(16)# emerge @preserved-rebuild ... calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 4) sci-chemistry/modeller-9.12-r3 from science * modeller-9.12.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking modeller-9.12.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.12-r3/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.12-r3/work ... >>> Installing (1 of 4) sci-chemistry/modeller-9.12-r3 * This package leaves a license Key file in /opt/modeller/modlib/modeller/config.py ... >>> Failed to emerge media-gfx/freecad-0.12.5284-r3, Log file: >>> '/var/tmp/portage/media-gfx/freecad-0.12.5284-r3/temp/build.log' * GNU info directory index is up-to-date. !!! existing preserved libs: >>> package: media-video/ffmpeg-1.2.4 * - /usr/lib64/libavutil.so.51 * - /usr/lib64/libavutil.so.51.73.101 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: media-libs/libjpeg-turbo-1.3.0-r2 * - /usr/lib64/libjpeg.so.8 * - /usr/lib64/libjpeg.so.8.0.2 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: sci-libs/hdf5-1.8.11 * - /usr/lib64/libhdf5.so.7 * - /usr/lib64/libhdf5.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.7 (sci-chemistry/modeller-9.12-r3) * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) * - /usr/lib64/libhdf5_hl.so.7 * - /usr/lib64/libhdf5_hl.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) ... >>> package: net-libs/serf-1.3.2 * - /usr/lib64/libserf-1.so.0 * - /usr/lib64/libserf-1.so.0.0.0 * used by /usr/lib64/libsvn_ra_serf-1.so.0.0.0 (dev-vcs/subversion-1.7.13) Use emerge @preserved-rebuild to rebuild packages using these libraries Could please try to remove modeller and reinstall it. I might be that a reemerge doesn't remove the preserved-libs. I did: root@leopard:/root(27)# qlist -Iv modeller sci-chemistry/modeller-9.12-r3 root@leopard:/root(28)# emerge -C modeller ... root@leopard:/root(29)# emerge -uvDN modeller ... >>> Recording sci-chemistry/modeller in "world" favorites file... >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. !!! existing preserved libs: >>> package: media-video/ffmpeg-1.2.4 * - /usr/lib64/libavutil.so.51 * - /usr/lib64/libavutil.so.51.73.101 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: media-libs/libjpeg-turbo-1.3.0-r2 * - /usr/lib64/libjpeg.so.8 * - /usr/lib64/libjpeg.so.8.0.2 * used by /usr/lib64/libvtkIO.so.5.10.1 (sci-libs/vtk-5.10.1) >>> package: sci-libs/hdf5-1.8.11 * - /usr/lib64/libhdf5.so.7 * - /usr/lib64/libhdf5.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.7 (sci-chemistry/modeller-9.12-r3) * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) * - /usr/lib64/libhdf5_hl.so.7 * - /usr/lib64/libhdf5_hl.so.7.0.4 * used by /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 (sci-chemistry/modeller-9.12-r3) * used by /usr/lib64/libvtkNetCDF.so.5.10.1 (sci-libs/vtk-5.10.1) So 'emerge @preserved-rebuild' will emerge again modeller. I still have the same problem. Any news? (In reply to Juergen Rose from comment #11) > I still have the same problem. Any news? I can't reproduce it. ANd I don't see the problem. WONTFIX because package has been moved to ::gentoo and removed from ::science |