Re: [phenixbb] Phenix installation on Debian9.6

9 Jan 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
 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
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