Your message dated Fri, 28 Jun 2024 14:35:57 +0000
with message-id <e1snchh-004id2...@fasolo.debian.org>
and subject line Bug#1072576: fixed in coot 1.1.09+dfsg-1
has caused the Debian Bug report #1072576,
regarding coot: save its states in HOME.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1072576: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1072576
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: coot
Version: 1.1.08+dfsg-3
Severity: normal
X-Debbugs-Cc: pi...@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
--- End Message ---
--- Begin Message ---
Source: coot
Source-Version: 1.1.09+dfsg-1
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
coot, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1072...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated coot package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 28 Jun 2024 10:04:00 -0400
Source: coot
Architecture: source
Version: 1.1.09+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1072576
Changes:
coot (1.1.09+dfsg-1) unstable; urgency=medium
.
* New upstream version 1.1.09+dfsg (Closes: #1072576)
* Disable sound on hurd-i386.
* Drop a0fbdb6c679b30c576f3ea8ff438f44ee50cc612.patch: integrated upstream.
Checksums-Sha1:
ef3dc0b6fde0ef2fc4694498e293e41eb0e70fa2 2964 coot_1.1.09+dfsg-1.dsc
38095897b8a626eb7be561f437cf76fe80c7d067 88499868 coot_1.1.09+dfsg.orig.tar.xz
94f32a32b6cddef572ff687db1a1829747e8b639 52448 coot_1.1.09+dfsg-1.debian.tar.xz
bdb4e2472cc111e6e9ff3f59bf91a0894c6facb7 12472
coot_1.1.09+dfsg-1_source.buildinfo
Checksums-Sha256:
50fc2bc2e0f87d5f953415ac89b99ec426d59b290c9382625cbe76af6ac4c10e 2964
coot_1.1.09+dfsg-1.dsc
1aff7fb1817d18c8de305c2e9822aaecd50fef76c3418c71607ad57381413b46 88499868
coot_1.1.09+dfsg.orig.tar.xz
72ceaaeb8d355f7dcf058f8994d73821fac4af4e98ebe2b34d2f38d1b7014471 52448
coot_1.1.09+dfsg-1.debian.tar.xz
e8f4a7183245cb115b6ffdf75b971e03264a9d9fb5b7474db36c128ca3a1c8be 12472
coot_1.1.09+dfsg-1_source.buildinfo
Files:
ead427ccbb127b92d0bbb6ef86084cc5 2964 science optional coot_1.1.09+dfsg-1.dsc
db95ea706d91fd17ea3bca76c3ece7f1 88499868 science optional
coot_1.1.09+dfsg.orig.tar.xz
c510eecd0cbcae42ac2ba26835f220c5 52448 science optional
coot_1.1.09+dfsg-1.debian.tar.xz
f7f9fa7ea1b5ac5a205172ddd34b1eda 12472 science optional
coot_1.1.09+dfsg-1_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=37pw
-----END PGP SIGNATURE-----
pgpEvcghDO67l.pgp
Description: PGP signature
--- End Message ---
