Summary: | [QA] file collision sci-biology/ncbi-tools++ & sci-libs/mmdb -- libmmdb.so | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Justin Lecher (RETIRED) <jlec> |
Component: | Current packages | Assignee: | Andrey Kislyuk (RETIRED) <weaver> |
Status: | RESOLVED FIXED | ||
Severity: | QA | CC: | binki, jlec, sci-biology, sci-chemistry |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Justin Lecher (RETIRED)
2010-01-12 10:34:04 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. 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? 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 Seems to be fixed as everything is working fine. Otherwise please reopen. |