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Today's Topics:
1. Re: Demeter on Ubuntu 14.04 (Ravel, Bruce)
----------------------------------------------------------------------
Message: 1
Date: Thu, 22 May 2014 13:09:14 +0000
From: "Ravel, Bruce"<bra...@bnl.gov>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Demeter on Ubuntu 14.04
Message-ID:<9ocjbe8obqgecedql4scmfu3.1400764153...@email.android.com>
Content-Type: text/plain; charset="us-ascii"
I'm on vacation right now and only have my tablet, so typing a decent response
is a challenge.
>From what you included, it looks as though you pulled or cloned the latest from within, but did not do the
"perl Build.pl" or "./Build installdeps" steps. If not starting from a clean install, it
may help to also "./Build touch_wrapper".
I'll be with email only sporadically for a while, unfortunately.
B
On May 21, 2014, at 11:27AM, Denis TESTEMALE wrote:
Dear members of the list,
it's that time of the (Linux) Ubuntu life cycles where you do upgrades and
break previously working programs... Upgrading to Ubuntu 14.04 made no
exception for me. It also broke the old Hephaestus programs, but I think it is
definitely time that I stop being lazy and switch to Demeter. So I'll focus on
the Demeter problems. Sorry about the lengthy post full of pasted error
messages.
--------------------------------------------------------------------------------------------------------------
Context: I'm running Ubuntu 64 bits 14.04. Demeter version 0.9.20. I followed
Ubuntu specific instructions found here:
https://gist.github.com/3959252
Demeter once worked but I cannot guarantee that it did just before the upgrade
to 14.04. After the upgrade, both trying to run dathena or to rebuild the
package ran into errors such as:
denis@huchet4:~/demeter$ ./Build
Building Demeter
Perl API version v5.14.0 of DateTime does not match v5.18.0 at
/usr/share/perl/5.18/XSLoader.pm line 92.
Compilation failed in require at lib/Xray/data/elam2st.PL line 405.
BEGIN failed--compilation aborted at lib/Xray/data/elam2st.PL line 405.
lib/Xray/data/elam2st.PL failed at
/home/denis/perl5/lib/perl5/Module/Build/Base.pm line 2963.
denis@huchet4:~/demeter$ dathena
Perl API version v5.14.0 of Wx does not match v5.18.0 at
/usr/lib/perl/5.18/DynaLoader.pm line 207.
Compilation failed in require at /home/denis/perl5/bin/dathena line 11.
BEGIN failed--compilation aborted at /home/denis/perl5/bin/dathena line 11.
-----------------------------------------------------------------------------------------------------------------------------------
So I erased the folders and reinstalled everything. The installation ran
smoothly (except I had to install missing deps several times, but no error
messages at the end). Now I can start the programs but run into problems:
For Dephaestus: everything works, I can plot f' and f" (gnuplot is working) but
when I try to plot some XANES references in the standards tab, it crashes with:
Attribute (bkg_nc0) does not pass the type constraint because: Validation
failed for 'LaxNum' with value 0,00000000000000 at
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37
Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)')
called at reader Moose::Exception::trace (defined at
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7
Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)')
called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49
Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)',
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm
line 128
Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xa44deb8)',
'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)',
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56
Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)',
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm
line 282
Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x9a3f0d8)',
'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27
Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint',
'type_constraint_message', 'Validation failed for \'LaxNum\' with value
0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0',
'value', '0,00000000000000') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm
line 52
Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint',
'type_constraint_message', 'Validation failed for \'LaxNum\' with value
0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0',
'value', '0,00000000000000') called at accessor Demeter::Data::bkg_nc0 (defined
at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm
line 309) line 4
Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xa372058)',
'0,00000000000000') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm
line 323
Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xa372058)') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line
674
Demeter::Data::_update('Demeter::Data=HASH(0xa372058)', 'fft') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm
line 24
Demeter::Data::Plot::plot('Demeter::Data=HASH(0xa372058)', 'E') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Standards.pm
line 267
Demeter::UI::Standards::plot('Demeter::UI::Standards=HASH(0x96b3d78)',
'Ferrihydrite', 'mu', 'plot') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm
line 139
Demeter::UI::Hephaestus::Standards::make_standards_plot('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)',
'Wx::CommandEvent=SCALAR(0x9a2ee50)',
'Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'mu') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm
line 79
Demeter::UI::Hephaestus::Standards::__ANON__('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)',
'Wx::CommandEvent=SCALAR(0x9a2ee50)') called at
/home/denis/perl5/bin/dhephaestus line 37
eval {...} at /home/denis/perl5/bin/dhephaestus line 37
Similar story and message (at least the first line, since the rest is a bit
obscure for me) for Dathena when I try to import a data file from an old Athena
.prj project (i.e., as far as I understand and remember things, a file where
there is no interactive import window to select columns, references, etc.).
Attribute (bkg_nc0) does not pass the type constraint because: Validation
failed for 'LaxNum' with value 68,42548963866604 at
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37
Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)')
called at reader Moose::Exception::trace (defined at
/usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7
Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)')
called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49
Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)',
'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm
line 128
Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xbd372b8)',
'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)',
'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56
Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)',
'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm
line 282
Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0xbd2d4c8)',
'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27
Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint',
'type_constraint_message', 'Validation failed for \'LaxNum\' with value
68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0',
'value', '68,42548963866604') called at
/usr/local/lib/perl/5.18.2/Moose/Util.pm line 52
Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint',
'type_constraint_message', 'Validation failed for \'LaxNum\' with value
68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0',
'value', '68,42548963866604') called at accessor Demeter::Data::bkg_nc0
(defined at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line
309) line 4
Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xbd3ec78)',
'68,42548963866604') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm
line 323
Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xbd3ec78)') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line
674
Demeter::Data::_update('Demeter::Data=HASH(0xbd3ec78)', 'fft') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm
line 24
Demeter::Data::Plot::plot('Demeter::Data=HASH(0xbd3ec78)', 'E') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm
line 209
Demeter::UI::Artemis::Prj::do_plot('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)',
'Demeter::Data::Prj=HASH(0xbd2a6a8)', 1) called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm
line 162
Demeter::UI::Artemis::Prj::plot_selection('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)',
'Wx::CommandEvent=SCALAR(0xbd31420)', 'Demeter::Data::Prj=HASH(0xbd2a6a8)',
'ARRAY(0xbd2bc78)', 'ARRAY(0xbd30f00)') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm
line 59
Demeter::UI::Artemis::Prj::__ANON__('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)',
'Wx::CommandEvent=SCALAR(0xbd31420)') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm
line 769
eval {...} at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm
line 769
Demeter::UI::Athena::IO::_prj('Demeter::UI::Athena=HASH(0xc7d498)',
'/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj',
'/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj', 1, '') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm
line 165
Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xc7d498)',
'/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj') called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm
line 793
Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0xa2feb60)',
'Wx::CommandEvent=SCALAR(0xbd27218)', 'Demeter::UI::Athena=HASH(0xc7d498)')
called at
/home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm
line 754
Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0xa2feb60)',
'Wx::CommandEvent=SCALAR(0xbd27218)') called at /home/denis/perl5/bin/dathena
line 39
eval {...} at /home/denis/perl5/bin/dathena line 39
Finally, still Dathena when I try to import a new data file (i.e., a file where I
expect an interactive import window to select the columns), there is no error
message in the shell, but in the bottom line of the Dathena GUI window, it says that
the file "cannot be read as data. (Do you need to enable a plugin?).
The thing is I never had to enable a plugin for such a data file (the data file
is the cu10k.dat file that you provided in the Ifeffit CD some time ago, and
you might still provide today).
OK, enough. Let me know if I can try different things to help source the
problem.
Regards.
Denis
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