[phenixbb] Phenix installation on Debian9.6

Billy Poon BKPoon at lbl.gov
Tue Jan 8 08:16:49 PST 2019 

Hi Danilo,

Another user on Debian 9 had a similar issue. What is the output to "locale
-a" and what is your LANG and LC_ALL environment variables set to? And in
the <phenix installation>/build/bin/phenix file, there is a place where
LC_ALL is set. What is LC_ALL set to in that file?

For unicode support, Phenix requires a language with UTF8 support (e.g.
en_GB.UTF-8). During the installation, Phenix tries to determine the locale
from the LC_ALL environment variable. By default, it gets set to
en_US.UTF-8 if nothing can be found. However, on Debian 9, I got an error
about en_GB even though en_US was available and set as the locale.

On my Debian 9.6 virtual machine, I have en_US.UTF-8 and en_GB.UTF-8
installed and my phenix installation is using en_US.UTF-8. If you want to
update the LC_ALL variable in the scripts in <phenix
installation>/build/bin,

1) Set LC_ALL to the language you want with UTF-8 support (e.g. "export
LC_ALL=en_US.UTF-8")
2) Run the "config_modules.sh" file in the <phenix installation>/build
directory to change all the scripts to use the new locale.

--
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 Tue, Jan 8, 2019 at 7:47 AM Danilo Belviso <danilo.belviso at ic.cnr.it>
wrote:

> Dear Rob,
>
> Thanks for your suggestions. I have just tried but it doesn't work,
> unfortunately.
>
> Thanks again.
>
> Regards,
>
> Danilo
>
> Il 2019-01-08 15:43 Robert Oeffner ha scritto:
> > Dear Danilo,
> >
> >
> > I encountered the same problem with the locale when installing Phenix
> > on Ubuntu on Windows 10. The solution was to do from a bash shell:
> >
> >
> > *cd /usr/share/locale*
> >
> > **
> >
> > *sudo locale-gen "en_GB.UTF-8"*
> >
> > **
> >
> > *sudo dpkg-reconfigure locales*
> >
> > I'm no linux expert so I wouldn't know if this procedure is general
> > enough that it would work on your system or if it would also solve the
> > other issues you mention before.
> >
> > Regards,
> >
> > Rob
> >
> >
> >
> > On 08/01/2019 14:32, Danilo Belviso wrote:
> >> Dear all,
> >>
> >> I am intalling phenix on my Debian 9.6.
> >>
> >> My arch is adm64 thus I downloaded the phenix version named Kernel 2.6
> >> (64-bit; CentOS 6).
> >>
> >> The installation procedure has been performed as suggested by the
> >> guide and no problems were obtained. However, by running phenix (after
> >> source phenix_env.sh) I get the follow output with several errors:
> >>
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion
> >> 'G_IS_LOADABLE_ICON (icon)' failed
> >> (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for
> >> stock: Failed to load icon
> >> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion
> >> 'pixbuf != NULL' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion
> >> 'G_IS_OBJECT (object)' failed
> >>
> >> Error in sys.excepthook:
> >> Traceback (most recent call last):
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py",
> >> line 886, in _excepthook
> >>     Error.show_exception_dialog(type, value, traceback)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Error.py",
> >> line 75, in show_exception_dialog
> >>     if (app.bug_timer.IsRunning() is False):
> >> AttributeError: 'PhenixApp' object has no attribute 'bug_timer'
> >>
> >> Original exception was:
> >> Traceback (most recent call last):
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py",
>
> >> line 23, in <module>
> >>     run(sys.argv[1:])
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py",
>
> >> line 17, in run
> >>     wxapp = App.PhenixApp(args)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py",
> >> line 70, in __init__
> >>     wx.App.__init__(self, 0)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py",
>
> >> line 8628, in __init__
> >>     self._BootstrapApp()
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py",
>
> >> line 8196, in _BootstrapApp
> >>     return _core_.PyApp__BootstrapApp(*args, **kwargs)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py",
> >> line 116, in OnInit
> >>     self.start_gui()
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py",
> >> line 144, in start_gui
> >>     callback_on_import=self.show_message)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py",
>
> >> line 280, in start_tracking
> >>     project_class="wxGUI2.Tracking.phenix_project_database", **kwds)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/__init__.py",
>
> >> line 19, in start_tracking
> >>     callback_on_import=callback_on_import)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py",
>
> >> line 117, in __init__
> >>     super(phenix_project_database, self).__init__(*args, **kwds)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py",
>
> >> line 39, in __init__
> >>     self.choose_project(try_current_dir=True)
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py",
>
> >> line 339, in choose_project
> >>     project_info = self.create_first_project()
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py",
>
> >> line 124, in create_first_project
> >>     from wxGUI2.Home import Projects
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Home/Projects.py",
>
> >> line 3, in <module>
> >>     from wxGUI2 import Base, Controls, PhilLayout, Windows, utils,
> >> Buttons
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/PhilLayout.py",
>
> >> line 5, in <module>
> >>     from wxGUI2 import Base, Controls, Windows, utils, PhilInterface,
> >> FileDisplay
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/FileDisplay.py",
>
> >> line 5, in <module>
> >>     import wxtbx.info_panels
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/info_panels.py",
>
> >> line 5, in <module>
> >>     import wxtbx.plots
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plots/__init__.py",
>
> >> line 21, in <module>
> >>     locale.setlocale(locale.LC_ALL, '')
> >>   File
> >>
> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/locale.py",
> >> line 581, in setlocale
> >>     return _setlocale(category, locale)
> >> locale.Error: unsupported locale setting
> >>
> >>
> >>
> >> Phenix starts by opening a window that states "locale 'en_GB' cannot
> >> be set" and abruptly closes so that I cannot use it.
> >>
> >> Do you have any suggestions to overcome such problems?
> >>
> >> I tried with Kernel 2.6 (64-bit; CentOS 5) and the 32-bit version too
> >> and the result is the same.
> >>
> >> Thanks in advance for your suggestions.
> >>
> >> Danilo
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >> Unsubscribe: phenixbb-leave at phenix-online.org
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