[Bug 472150] Review Request: coot - crystallographic macromolecular building toolkit
bugzilla at redhat.com
bugzilla at redhat.com
Tue Mar 24 23:16:26 UTC 2009
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https://bugzilla.redhat.com/show_bug.cgi?id=472150
--- Comment #15 from Jason Tibbitts <tibbs at math.uh.edu> 2009-03-24 19:16:04 EDT ---
Indeed this does build. Here's the complete rpmlint listing; I'm sorry for
any terrible line wrapping; this is big enough that I'm working in an external
editor.
coot.x86_64: W: name-repeated-in-summary Coot
Please don't include the name of the package in the summary.
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-tw.so.0.0.0
/lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-skeleton.so.0.0.0 /usr/lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-skeleton.so.0.0.0 /usr/lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-skeleton.so.0.0.0 /usr/lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-skeleton.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libccp4mg-surface.so.0.0.0 /usr/lib64/libgpp4.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-ideal.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libgsl.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-coord-extras.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-db-main.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-high-res.so.0.0.0 /usr/lib64/libccp4mg-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-utils.so.0.0.0 /lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libart_lgpl_2.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libcairo.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libpango-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /lib64/libgmodule-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libcoot-atomutils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libclipper.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-sequence-view.so.0.0.0 /lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-isosurface.so.0.0.0 /usr/lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-isosurface.so.0.0.0 /usr/lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-isosurface.so.0.0.0 /usr/lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-isosurface.so.0.0.0 /usr/lib64/libmmdb.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-isosurface.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-map-utils.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-analysis.so.0.0.0 /usr/lib64/libclipper.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-analysis.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-map-heavy.so.0.0.0 /usr/lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-map-heavy.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-atomutils.so.0.0.0 /lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-cabuild.so.0.0.0 /usr/lib64/libmmdb.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-ligand.so.0.0.0 /usr/lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-ligand.so.0.0.0 /usr/lib64/libgsl.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-ligand.so.0.0.0 /usr/lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-mini-mol.so.0.0.0 /usr/lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libglut.so.3
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libXmu.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libgtk-x11-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libgdk-x11-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libcairo.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libpango-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgobject-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgmodule-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /lib64/libglib-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-surface.so.0.0.0 /usr/lib64/libgpp4.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-ideal.so.0.0.0 /usr/lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency
/usr/lib64/libcoot-coords.so.0.0.0 /usr/lib64/libclipper.so.2
Did you consider cleaning these up at all?
coot.x86_64: W: shared-lib-calls-exit /usr/lib64/libcoot-coords.so.0.0.0
exit at GLIBC_2.2.5
coot.x86_64: W: shared-lib-calls-exit /usr/lib64/libcoot-map-heavy.so.0.0.0
exit at GLIBC_2.2.5
coot.x86_64: W: shared-lib-calls-exit /usr/lib64/libcoot-ligand.so.0.0.0
exit at GLIBC_2.2.5
These are bugs and should be reported upstream, but they aren't blockers.
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0 _ZN15graphics_info_t9moleculesE
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0 _ZN21molecule_class_info_t9makebondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0
_ZN21molecule_class_info_t45initialize_coordinate_things_on_read_moleculeESs
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0 _ZN21molecule_class_info_t9makebondsEv
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0 _ZN21molecule_class_info_t9makebondsEf
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-skeleton.so.0.0.0
_ZN21molecule_class_info_t13make_ca_bondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0 _ZN15graphics_info_t9moleculesE
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN21molecule_class_info_t9makebondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN21molecule_class_info_t45initialize_coordinate_things_on_read_moleculeESs
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN21molecule_class_info_t9makebondsEv
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN21molecule_class_info_t9makebondsEf
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN21molecule_class_info_t13make_ca_bondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN15graphics_info_t32update_things_on_move_and_redrawEv
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN15graphics_info_t30try_centre_from_new_go_to_atomEv
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN15graphics_info_t23set_go_to_atom_moleculeEi
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0 set_sequence_view_is_displayed
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-sequence-view.so.0.0.0
_ZN15graphics_info_t29set_go_to_residue_intelligentERKSsiS1_
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0 _ZN15graphics_info_t9moleculesE
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0 _ZN21molecule_class_info_t9makebondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0
_ZN21molecule_class_info_t45initialize_coordinate_things_on_read_moleculeESs
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0 _ZN21molecule_class_info_t9makebondsEv
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0 _ZN21molecule_class_info_t9makebondsEf
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-atomutils.so.0.0.0
_ZN21molecule_class_info_t13make_ca_bondsEff
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-coord-extras.so.0.0.0
_ZN4coot16protein_geometry15try_dynamic_addERKSsi
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-coord-extras.so.0.0.0
_ZNK4coot16protein_geometry22get_monomer_restraintsERKSs
coot.x86_64: W: undefined-non-weak-symbol
/usr/lib64/libcoot-coord-extras.so.0.0.0
_ZN4coot16protein_geometry32have_dictionary_for_residue_typeERKSsi
Did you consider cleaning these up at all, by properly linking the libraries
together?
coot-debuginfo.x86_64: E: script-without-shebang
/usr/src/debug/coot-0.5.2/ccp4mg-utils/cartesian.cc
coot-debuginfo.x86_64: E: script-without-shebang
/usr/src/debug/coot-0.5.2/src/coot_pythonmodule.cc
coot-debuginfo.x86_64: E: script-without-shebang
/usr/src/debug/coot-0.5.2/coot-surface/rgbreps.cc
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXFortranFile.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTriangle.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXSurface.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXChargeTable.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXSurfaceVertex.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXCoord.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXFFTSolventMap.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTorusNode.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXSurface.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXCoord.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/TokenIterator.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTriangle.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTorusNode.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/coot-surface/rgbreps.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTorusElement.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/ccp4mg-utils/cartesian.h
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXQADSurface.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXFortranFile.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXFFTSolventMap.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXTorusElement.cpp
coot-debuginfo.x86_64: W: spurious-executable-perm
/usr/src/debug/coot-0.5.2/surface/CXXSurfaceVertex.h
These all stem from the fact that bits of the source are executable. I can't
imagine why the source code would need to be executable; can you run a
find/chmod over it in %prep to clean this up?
coot-devel.x86_64: W: no-documentation
This is OK.
Some other comments:
I'm unsure of the license of this package. You indicate that it's GPLv2 only.
COPYING contains GPLv3 (which doesn't generally mean that the source is
actually under version 3). The source seems to be a mix of GPLv3+ and GPLv2+,
LGPLv2+. For example, run
grep -r 'version.*of the' *
and see what you get. There's too much code for me to do a full license
review here; you'll need to see what source files are compiled into which
binaries and object files and compute the results of those license
combinations for each binary and each standalone file. If they aren't all the
same, you'll need to provide a breakdown. See
http://fedoraproject.org/wiki/Licensing and
http://fedoraproject.org/wiki/Packaging/LicensingGuidelines for more
information.
Also, I'm not sure it's OK to just pull the contents of
coot-guile-extras.tar.gz from other upstream packages; they each have their
own attributions and, I believe, different licensing terms. For example,
goosh.scm is GPL but no version is given, which means we can choose any
version, so its license is GPL+. Is there any reason not to just use the
pristine original tarballs for those files? If you don't need the included
buildsystems you can just pick the files you need, but you may also need to
include documentation and license files.
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