Bug#1072576: coot: save its states in HOME.
Picca Frédéric-Emmanuel
picca at debian.org
Tue Jun 4 16:31:25 BST 2024
Package: coot
Version: 1.1.08+dfsg-3
Severity: normal
X-Debbugs-Cc: picca at debian.org
Dear Maintainer,
While using coot I found that it save it's states in these files
DEBUG:: saving state to filename 0-coot.state.py
State file 0-coot.state.py written.
State file 0-coot-history.py written.
State file 0-coot-history.scm written.
Maybe this is just something linked to a DEBUG mode.... It would be
great if this state could be saved in the xdg cache directory, or
maybe create a Release coot without all the Debuging.
I do not know what is the best solution...
The coot command line is quite verbose...
I am wondering if these warnings are important ?
Cheers
Frederic
:~$ coot
INFO:: built with GTK 4.12.5
pdd /usr/share/coot
WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIR /usr/share/coot/lib failed to find the monomer library
WARNING:: COOT_PREFIX set, but no dictionary lib found
WARNING: Failed to read restraints dictionary.
debug:: in setup_python() pydirectory is /usr/lib/python3.11/site-packages
debug:: in setup_python() pkgpydirectory is /usr/lib/python3.11/site-packages/coot
WARNING:: The reference structures directory (COOT_REF_STRUCTS): /usr/share/coot/reference-structures was not found.
Ca->Mainchain will not be possible.
WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIR /usr/share/coot/lib failed to find the monomer library
WARNING:: COOT_PREFIX set, but no dictionary lib found
WARNING: Failed to read restraints dictionary.
INFO:: GL Version: 4.2 (Core Profile) Mesa 24.1.0-2
INFO:: GL Shading Language Version: 4.20
INFO:: GL Renderer: Mesa Intel(R) HD Graphics 2500 (IVB GT1)
INFO:: GL Vendor: Intel
Shader compile meshes-with-shadows.shader success
Shader compile meshes-for-shadow-map.shader success
Shader compile instanced-meshes-for-shadow-map.shader success
Shader compile meshes-for-ssao.shader success
Shader compile instanced-meshes-for-ssao.shader success
Shader compile texture-meshes-for-ssao.shader success
Shader compile texture-meshes-with-shadows.shader success
Shader compile texture-meshes-shadow-map.shader success
Shader compile texture-meshes.shader success
Shader compile shadow-map-image-texture.shader success
Shader compile 9.ssao_geometry.shader success
Shader compile 9.ssao.shader success
Shader compile 9.ssao_blur.shader success
Shader compile instanced-meshes-with-shadows.shader success
Shader compile outline-of-active-residue.shader success
Shader compile map.shader success
Shader compile draw-map-cap.shader success
Shader compile model.shader success
Shader compile central-cube.shader success
Shader compile central-cube.shader success
Shader compile hud-text.shader success
Shader compile hud-bars.shader success
Shader compile hud-labels.shader success
Shader compile hud-image-texture.shader success
Shader compile atom-label.shader success
Shader compile moleculestotriangles.shader success
Shader compile lines.shader success
Shader compile lines-pulse.shader success
Shader compile rama-balls.shader success
Shader compile particles.shader success
Shader compile instanced-objects.shader success
Shader compile extra-distance-restraints.shader success
Shader compile hud-geometry-tooltip-text.shader success
Shader compile residue-markers.shader success
Shader compile residue-markers-for-ssao.shader success
Shader compile ligand-view.shader success
Shader compile model-as-mesh.shader success
Shader compile symmetry-atoms-lines.shader success
Shader compile hud-bars.shader success
Shader compile rama-plot-axes-and-ticks.shader success
Shader compile rama-plot-phi-psi-markers.shader success
Shader compile hud-lines.shader success
Shader compile background-image.shader success
Shader compile meshes.shader success
Shader compile texture-meshes.shader success
Shader compile effects.shader success
Shader compile blur-x.shader success
Shader compile blur-y.shader success
Shader compile depth-of-field.shader success
Shader compile rotation-centre-cross-hairs-for-ssao.shader success
GL ERROR:: attach_buffers() --- post gtk_gl_area_attach_buffers() with gl_area 0x55c678c94a80 calling function: new_startup_realize()
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c6769bc670 of type GtkToggleButton: The parent widget that wraps GtkToggleButton::child is not a GtkBox but a GtkToggleButton. GtkToggleButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c6763cdd20 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c6769cffd0 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c676f92da0 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c676f97bd0 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c676faf000 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
** (Coot:16753): WARNING **: 17:25:52.581: set_vertical_toolbar_internal_alignment: Toolbar item 0x55c676fbcda0 of type GtkMenuButton: The parent widget that wraps GtkMenuButton::child is not a GtkBox but a GtkGizmo. GtkMenuButton::child however is a GtkBox. Attempt will be made to align it. It might not work.
DEBUG:: --- new_startup_on_glarea_resize() 893 905
int max 2147483647 46341
DEBUG:: reset_frame_buffers() 893 905 use_framebuffers: 1
debug:: reset_frame_buffers() with sf 1 893 x 905
DEBUG:: --- new_startup_on_glarea_resize() 653 882
int max 2147483647 46341
DEBUG:: reset_frame_buffers() 653 882 use_framebuffers: 1
debug:: reset_frame_buffers() with sf 1 653 x 882
---------------------------------------- run_command_line_scripts() ----------------
DEBUG:: saving state to filename 0-coot.state.py
State file 0-coot.state.py written.
State file 0-coot-history.py written.
State file 0-coot-history.scm written.
-- System Information:
Debian Release: trixie/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 6.7.12-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages coot depends on:
ii coot-data 1.1.08+dfsg-3
ii gir1.2-gtk-4.0 4.12.5+ds-6+b1
ii libasound2t64 1.2.11-1+b1
ii libblas3 [libblas.so.3] 3.12.0-3
ii libboost-python1.83.0 [libboost-python1.83.0-py31 1.83.0-3
1]
ii libc6 2.38-12
ii libcairo2 1.18.0-3+b1
ii libclipper2 2.1.20201109-2+b2
ii libcootapi1.1 1.1.08+dfsg-3
ii libcurl3t64-gnutls 8.8.0-1
ii libepoxy0 1.5.10-1+b2
ii libfreetype6 2.13.2+dfsg-1+b4
ii libgcc-s1 14.1.0-1
ii libgdk-pixbuf-2.0-0 2.42.12+dfsg-1
ii libglib2.0-0t64 2.80.2-2
ii libgomp1 14.1.0-1
ii libgraphene-1.0-0 1.10.8-3+b1
ii libgsl27 2.7.1+dfsg-6+b1
ii libgtk-4-1 4.12.5+ds-6+b1
ii libmmdb2-0 2.0.22-1+b1
ii libopenblas0-pthread [libblas.so.3] 0.3.27+ds-2
ii libpango-1.0-0 1.52.2+ds-1
ii libpangocairo-1.0-0 1.52.2+ds-1
ii libpng16-16t64 1.6.43-5
ii libpython3.11t64 3.11.9-1
ii librdkit1t64 202309.3-4
ii libsqlite3-0 3.46.0-1
ii libssm2 1.4.0-2+b2
ii libstdc++6 14.1.0-1
ii libvorbisfile3 1.3.7-2
ii python3 3.11.8-1
ii python3-gi 3.48.2-1
ii python3-rdkit 202309.3-4
ii refmac-dictionary 5.41-2
ii zlib1g 1:1.3.dfsg+really1.3.1-1
coot recommends no packages.
Versions of packages coot suggests:
pn coot-doc <none>
-- no debconf information
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