gtk glib error messages and too large fonts when starting phenix 1.11.1-2575
Dear colleagues, Today I install latest stable phenix 1.11.1-2575 without problems - output attached. When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix. Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI? Best regards, Martin ############### my Glib Gtk error messages ############## [x_marmo@triolith2 ~]$ phenix (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed Already checked for new versions in last 24 hours, skipping Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: [email protected]
Dear colleagues, Allow me to share a workaround created by Sebastian Thorarensen for the issue described below Best regards, Martin ############# Email from Sebastian Thorarensen NSC ################## Hi Martin that error message mean Phenix fail to load certain icons and if comparing Phenix 1.11.1 with 1.10.1 there is an icon missing on OK-button when starting Phenix Phenix is packaged with GTK and wxWidgets (an abstraction layer for GTK for instance). It is also packaged with a windows theme that Phenix tell GTK to use. It fail however to tell GTK to use the icons that follow the theme, and instead an icon theme named gnome is used. gnome is incomplete; for instance an OK-icon is missing, however that does not matter, since GTK has build-in icons that can be used when missing in the selected icon-theme. In Phenix 1.11.1 they updated GTK and wxWidgets. When doing so it appear that GTKs built-in icons were broken. It could be a bug either in Phenix, GTK or wxWidgets. I cannot find where the issue originates. The following workaround tricks Phenix to use its build-in icon theme, instead of the GTK ones that does not work # Goto Phenix installation directory cd /proj/xray/software/phenix/phenix-1.11.1-2575 # Goto Phenix icon folder cd base/share/icons # Copy systems gnome theme to this floder cp -r /usr/share/icons/gnome . # Copy Phenix icon theme into the "gnome" theme cp -r Clearlooks/16x16/gtk/* gnome/16x16/stock/generic cp -r Clearlooks/24x24/gtk/* gnome/24x24/stock/generic # Update the icon cache gtk-update-icon-cache gnome This is almost enough. Phenix startup script sets the path to its build in themes incorrect so we need to fix that as well as: In /proj/xray/software/phenix/phenix-1.11.1-2575/build/bin/phenix please change XDG_DATA_DIRS=$CCTBX_BUILD_BASE/base/share into XDG_DATA_DIRS=$CCTBX_BUILD_BASE/share I tested this at my own Phenix installation and it removes all error messages and make all icons visible. Why the text is bigger in version 1.11.1 I do not know however it fits with https://www.phenix-online.org/documentation/images/gui_main.png so I think nothing is wrong here. -- Med vänliga hälsningar, Sebastian From: [email protected] [mailto:[email protected]] On Behalf Of Martin Moche Sent: den 16 november 2016 16:45 To: [email protected] Subject: [phenixbb] gtk glib error messages and too large fonts when starting phenix 1.11.1-2575 Dear colleagues, Today I install latest stable phenix 1.11.1-2575 without problems - output attached. When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix. Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI? Best regards, Martin ############### my Glib Gtk error messages ############## [x_marmo@triolith2 ~]$ phenix (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed Already checked for new versions in last 24 hours, skipping Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: [email protected]mailto:[email protected]
Hi Martin and Sebastian,
Thanks for the tip. I knew that the warnings started appearing after the
dependency updates, but I prioritized other issues for the release since it
wasn't a fatal error. I'll get this fixed soon.
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Fri, Nov 18, 2016 at 7:46 AM, Martin Moche
Dear colleagues,
Allow me to share a workaround created by Sebastian Thorarensen for the issue described below
Best regards,
Martin
############# Email from Sebastian Thorarensen NSC ##################
Hi Martin
that error message mean Phenix fail to load certain icons and if comparing Phenix 1.11.1 with 1.10.1 there is an icon missing on OK-button when starting Phenix
Phenix is packaged with GTK and wxWidgets (an abstraction layer for GTK for instance). It is also packaged with a windows theme that Phenix tell GTK to use. It fail however to tell GTK to use the icons that follow the theme, and instead an icon theme named gnome is used. gnome is incomplete; for instance an OK-icon is missing, however that does not matter, since GTK has build-in icons that can be used when missing in the selected icon-theme.
In Phenix 1.11.1 they updated GTK and wxWidgets. When doing so it appear that GTKs built-in icons were broken. It could be a bug either in Phenix, GTK or wxWidgets. I cannot find where the issue originates.
The following workaround tricks Phenix to use its build-in icon theme, instead of the GTK ones that does not work
# Goto Phenix installation directory
cd /proj/xray/software/phenix/phenix-1.11.1-2575
# Goto Phenix icon folder
cd base/share/icons
# Copy systems gnome theme to this floder
cp -r /usr/share/icons/gnome .
# Copy Phenix icon theme into the ”gnome” theme
cp -r Clearlooks/16x16/gtk/* gnome/16x16/stock/generic
cp -r Clearlooks/24x24/gtk/* gnome/24x24/stock/generic
# Update the icon cache
gtk-update-icon-cache gnome
This is almost enough. Phenix startup script sets the path to its build in themes incorrect so we need to fix that as well as:
In /proj/xray/software/phenix/phenix-1.11.1-2575/build/bin/phenix please change
XDG_DATA_DIRS=$CCTBX_BUILD_BASE/base/share
into
XDG_DATA_DIRS=$CCTBX_BUILD_BASE/share
I tested this at my own Phenix installation and it removes all error messages and make all icons visible. Why the text is bigger in version 1.11.1 I do not know however it fits with https://www.phenix-online.org/ documentation/images/gui_main.png so I think nothing is wrong here.
--
Med vänliga hälsningar,
Sebastian
*From:* [email protected] [mailto:phenixbb-bounces@ phenix-online.org] *On Behalf Of *Martin Moche *Sent:* den 16 november 2016 16:45 *To:* [email protected] *Subject:* [phenixbb] gtk glib error messages and too large fonts when starting phenix 1.11.1-2575
Dear colleagues,
Today I install latest stable phenix 1.11.1-2575 without problems - output attached.
When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below
These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix.
Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI?
Best regards, Martin
############### my Glib Gtk error messages ##############
[x_marmo@triolith2 ~]$ phenix
(main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed
(main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon
(main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed
(main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed
(main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed
(main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon
(main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed
(main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed
Already checked for new versions in last 24 hours, skipping
Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: [email protected]
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participants (2)
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Billy Poon -
Martin Moche