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Bug 300690 - [QA] file collision sci-biology/ncbi-tools++ & sci-libs/mmdb -- libmmdb.so
Summary: [QA] file collision sci-biology/ncbi-tools++ & sci-libs/mmdb -- libmmdb.so
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High QA (vote)
Assignee: Andrey Kislyuk (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2010-01-12 10:34 UTC by Justin Lecher (RETIRED)
Modified: 2010-06-26 11:08 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---

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Description Justin Lecher (RETIRED) gentoo-dev 2010-01-12 10:34:04 UTC 
Is that the same lib and could ncbi++ depend on sci-libs/mmdb.
Comment 1 Andrey Kislyuk (RETIRED) gentoo-dev 2010-02-26 17:29:34 UTC 
Hi Justin,

FYI, I've set ncbi-tools++ to use its own subdirectory of /usr/lib and the files no longer collide.

That said, I'm still unclear on whether this is the same code - no time to figure that out at the moment.
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2010-02-26 17:43:32 UTC 
Big thanks for that. I want to add psipred, which depends on ncbi++, but many crystalographic programs depend on mmdb. Do I see it right thar ncbi++ doesn't install headers?
Comment 3 Andrey Kislyuk (RETIRED) gentoo-dev 2010-02-26 18:18:11 UTC 
It installs headers, but they're different headers. And judging from that, i think it's different code. The block might have to stay - I'm not sure how ld filename resolution works for libraries - if it has two files with the same name but different contents, will it know which library to load for different executables?

onyx objects # equery files ncbi-tools++|grep mmdb
/usr/include/ncbi-tools++/objects/mmdb1
/usr/include/ncbi-tools++/objects/mmdb1/.cvsignore
/usr/include/ncbi-tools++/objects/mmdb1/Atom.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_pntr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_pntr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_pntr_set.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Atom_pntr_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biomol_descr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biomol_descr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biost_resid_graph_set_pntr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biost_resid_graph_set_pntr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_annot_set.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_annot_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_descr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_descr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_graph.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_graph_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_graph_pntr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_graph_pntr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_history.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_history_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_replace.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_replace_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_residue_graph_set.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_residue_graph_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_set.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_source.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Biostruc_source_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Chiral_center.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Chiral_center_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Inter_residue_bond.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Inter_residue_bond_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Intra_residue_bond.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Intra_residue_bond_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/MMDB_Chemical_graph_module.hpp
/usr/include/ncbi-tools++/objects/mmdb1/MMDB_module.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Mmdb_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Mmdb_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Molecule_graph.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Molecule_graph_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Molecule_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Molecule_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/PCSubstance_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/PCSubstance_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph_pntr.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_graph_pntr_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_id.hpp
/usr/include/ncbi-tools++/objects/mmdb1/Residue_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb1/mmdb1__.hpp
/usr/include/ncbi-tools++/objects/mmdb2
/usr/include/ncbi-tools++/objects/mmdb2/.cvsignore
/usr/include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Anisotro_temperatu_factors.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Anisotro_temperatu_factors_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_coordinates.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_coordinates_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_occupancies.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_occupancies_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_temperature_factors.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Atomic_temperature_factors_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Biostruc_model.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Biostruc_model_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Conformation_ensemble.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Conformation_ensemble_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Coordinates.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Coordinates_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Density_coordinates.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Density_coordinates_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Isotropi_temperatu_factors.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Isotropi_temperatu_factors_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/MMDB_Structural_model_module.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_coordinate_set.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_coordinate_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_coordinate_set_id.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_coordinate_set_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_descr.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_descr_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_id.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_space.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_space_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_space_points.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_space_points_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_type.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Model_type_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Reference_frame.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Reference_frame_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Surface_coordinates.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Surface_coordinates_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/T_mesh.hpp
/usr/include/ncbi-tools++/objects/mmdb2/T_mesh_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Triangles.hpp
/usr/include/ncbi-tools++/objects/mmdb2/Triangles_.hpp
/usr/include/ncbi-tools++/objects/mmdb2/mmdb2__.hpp
/usr/include/ncbi-tools++/objects/mmdb3
/usr/include/ncbi-tools++/objects/mmdb3/.cvsignore
/usr/include/ncbi-tools++/objects/mmdb3/Align_stats.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Atom_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_id.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set_descr.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set_descr_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set_id.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_feature_set_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_script.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_script_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_script_step.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Biostruc_script_step_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Brick.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Brick_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Camera.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Camera_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Chem_graph_alignment.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Chem_graph_alignment_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Chem_graph_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Chem_graph_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Color_prop.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Color_prop_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Cone.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Cone_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Cylinder.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Cylinder_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/GL_matrix.hpp
/usr/include/ncbi-tools++/objects/mmdb3/GL_matrix_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/MMDB_Features_module.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Model_space_point.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Model_space_point_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Molecule_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Molecule_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Move.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Move_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Other_feature.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Other_feature_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/RealValue.hpp
/usr/include/ncbi-tools++/objects/mmdb3/RealValue_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_boundary.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_boundary_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_coordinates.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_coordinates_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_similarity.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Region_similarity_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Render_prop.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Render_prop_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_explicit_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_explicit_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_interval_pntr.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_interval_pntr_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_pntrs.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Residue_pntrs_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Rot_matrix.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Rot_matrix_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Sphere.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Sphere_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Step_id.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Step_id_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Trans_matrix.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Trans_matrix_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Transform.hpp
/usr/include/ncbi-tools++/objects/mmdb3/Transform_.hpp
/usr/include/ncbi-tools++/objects/mmdb3/mmdb3__.hpp
/usr/lib64/ncbi-tools++/libmmdb.so
onyx objects # equery files mmdb
[ Searching for packages matching mmdb... ]
* Contents of sci-libs/mmdb-1.21:
/usr
/usr/include
/usr/include/mmdb
/usr/include/mmdb/bfgs_min.h
/usr/include/mmdb/file_.h
/usr/include/mmdb/hybrid_36.h
/usr/include/mmdb/linalg_.h
/usr/include/mmdb/machine_.h
/usr/include/mmdb/math_.h
/usr/include/mmdb/mattype_.h
/usr/include/mmdb/mmdb_align.h
/usr/include/mmdb/mmdb_atom.h
/usr/include/mmdb/mmdb_bondmngr.h
/usr/include/mmdb/mmdb_chain.h
/usr/include/mmdb/mmdb_cifdefs.h
/usr/include/mmdb/mmdb_coormngr.h
/usr/include/mmdb/mmdb_cryst.h
/usr/include/mmdb/mmdb_defs.h
/usr/include/mmdb/mmdb_ficif.h
/usr/include/mmdb/mmdb_file.h
/usr/include/mmdb/mmdb_graph.h
/usr/include/mmdb/mmdb_manager.h
/usr/include/mmdb/mmdb_mask.h
/usr/include/mmdb/mmdb_mmcif.h
/usr/include/mmdb/mmdb_model.h
/usr/include/mmdb/mmdb_rwbrook.h
/usr/include/mmdb/mmdb_sbase.h
/usr/include/mmdb/mmdb_sbase0.h
/usr/include/mmdb/mmdb_selmngr.h
/usr/include/mmdb/mmdb_symop.h
/usr/include/mmdb/mmdb_tables.h
/usr/include/mmdb/mmdb_title.h
/usr/include/mmdb/mmdb_uddata.h
/usr/include/mmdb/mmdb_utils.h
/usr/include/mmdb/mmdb_xml.h
/usr/include/mmdb/random_n.h
/usr/include/mmdb/stream_.h
/usr/lib64
/usr/lib64/libmmdb.a
/usr/lib64/libmmdb.la
/usr/lib64/libmmdb.so -> libmmdb.so.0.0.0
/usr/lib64/libmmdb.so.0 -> libmmdb.so.0.0.0
/usr/lib64/libmmdb.so.0.0.0
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2010-06-26 11:08:35 UTC 
Seems to be fixed as everything is working fine. Otherwise please reopen.