[Ifeffit] Demeter on Ubuntu 14.04

Mon May 26 09:11:51 CDT 2014

Thanks for your answer Bruce.
Don't spoil your holidays/vacation for this! I had done the "perl 
Build.pl" or "./Build installdeps" steps. In fact I tried a clean 
install with all those steps.
Right now, I tried the touch_wrapper you mentionned without success. I 
also tried an install as root for all the steps: no success either.

I'm stuck and it might be something stupid I can't see. When you have 
some time to have a look, let me know, there's no rush right now.

Cheers
denis

Le 22/05/2014 15:09, ifeffit-request at millenia.cars.aps.anl.gov a écrit :
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>     1. Re: Demeter on Ubuntu 14.04 (Ravel, Bruce)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 22 May 2014 13:09:14 +0000
> From: "Ravel, Bruce"<bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit<ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Demeter on Ubuntu 14.04
> Message-ID:<9ocjbe8obqgecedql4scmfu3.1400764153184 at 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 at 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 at 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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