[phenixbb] Phenix installation on Debian9.6

Wed Jan 9 00:30:23 PST 2019

Dear Danilo,

I agree that the language settings are probably not the cause of the problem.

Maybe phenix created a segmentation fault. On recent versions of Debian, these 
show in the output of dmesg, but not necessarily in the terminal where you 
started phenix.

Run phenix again, then type 'dmesg -T'  to check if there is a segmentation 
fault.

Best,
Tim

On Wednesday, January 9, 2019 9:15:39 AM CET Danilo Belviso wrote:
> 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-package
> > s/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-package
> > s/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/Proj
> > ects.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/PhilLayou
> > t.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/FileDispl
> > ay.py",> 
> >>>> line 5, in <module>
> >>>> import wxtbx.info_panels
> >>>> File
> > 
> > "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/inf
> > o_panels.py",> 
> >>>> line 5, in <module>
> >>>> import wxtbx.plots
> >>>> File
> > 
> > "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plo
> > ts/__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
> >> 
> >> _______________________________________________
> >> 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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> phenixbb at phenix-online.org
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-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

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