Re: [phenixbb] Phenix installation on Debian9.6

9 Jan 2019

      Hi Danilo,

I have a Debian 9.6 virtual machine running and Phenix is working after
en_GB is installed. The problem is with the locale. It looks like en_GB is
required even though another language is used. I had to install en_GB even
if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB
error. After installing en_GB, the GUI works normally (see attached
screenshot, phenix.png).

To install en_GB with instructions from https://wiki.debian.org/Locale,
1) open a Terminal and become root
2) run "dpkg-reconfigure locales"
3) Select en_GB.UTF-8 (see attached screenshot, locale.png)
4) Select "OK" and complete process. You'll have to just choose your
default language, but you should have it_IT.UTF-8 as your default
5) Verify that en_GB is available with "locale -a" (Mine is shown in a
terminal in phenix.png)

Changing the setting for Phenix
1) Go to the <phenix installation>/build directory
2) Type "export LC_ALL=it_IT.UTF-8"
3) Run the config_modules.sh script
4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I
check that <phenix installation>/build/bin/phenix has LC_ALL set to
it_IT.UTF-8
5) Phenix should run and the main GUI should pop up

I suspect that because Phenix is not localized, we may be requiring an
English language to be installed and maybe en_GB is a default. So in
phenix.png, the dates for the projects are in Italian, but everything else
is in English. Also, I think our number formatting is not localized, so
decimal points will be "." instead of ",".

I'm sending the images to you directly since the bulletin board has some
size limit and the original message with attached images is waiting
approval.

--
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 Wed, Jan 9, 2019 at 8:53 AM Billy Poon  wrote:
...
Hi Danilo,
I have a Debian 9.6 virtual machine running and Phenix is working after
en_GB is installed. The problem is with the locale. It looks like en_GB is
required even though another language is used. I had to install en_GB even
if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB
error. After installing en_GB, the GUI works normally (see attached
screenshot, phenix.png).
To install en_GB with instructions from https://wiki.debian.org/Locale,
1) open a Terminal and become root
2) run "dpkg-reconfigure locales"
3) Select en_GB.UTF-8 (see attached screenshot, locale.png)
4) Select "OK" and complete process. You'll have to just choose your
default language, but you should have it_IT.UTF-8 as your default
5) Verify that en_GB is available with "locale -a" (Mine is shown in a
terminal in phenix.png)
Changing the setting for Phenix
1) Go to the <phenix installation>/build directory
2) Type "export LC_ALL=it_IT.UTF-8"
3) Run the config_modules.sh script
4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I
check that <phenix installation>/build/bin/phenix has LC_ALL set to
it_IT.UTF-8
5) Phenix should run and the main GUI should pop up
I suspect that because Phenix is not localized, we may be requiring an
English language to be installed and maybe en_GB is a default. So in
phenix.png, the dates for the projects are in Italian, but everything else
is in English. Also, I think our number formatting is not localized, so
decimal points will be "." instead of ",".
--
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 Wed, Jan 9, 2019 at 12:32 AM Tim Gruene  wrote:
...
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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--
Paul Scherrer Institut
Tim Gruene
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CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
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