[phenixbb] Phenix installation on Debian9.6
Danilo Belviso
danilo.belviso at ic.cnr.it
Wed Jan 9 00:15:39 PST 2019
Dear Billy K. Poon,
Thanks for your suggestion. My LANG variable is it_IT.UTF-8 and LC_ALL
in /build/bin/phenix is en_US.UTF-8. Unfortunately, once changed the
variable, reconfiguration as suggested doesn't fix up the problem. I
would like to say that the problem/warning related to "locale 'en_GB'
cannot be set" is just one of that shown in my first email. Likely, it
is also the less important. Indeed, I always had the same problem with
previous versions of phenix. The difference is that in that case phenix
worked and now it stops abruptly. It is just my opinion but the problem
could be in the list I posted in the first email.
Thanks again for your suggestions.
Regards,
Danilo
Il 2019-01-08 17:16 Billy Poon ha scritto:
> 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
>>>> _______________________________________________
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