[Ifeffit] Installation problems for Demeter on Ubuntu 16.04

Jo Melville melville at mit.edu
Wed Nov 13 22:21:24 CST 2019


Thank you for your advice, Bruce. After trying a few things that didn't
work (I already had Wx installed through apt, so that wasn't the culprit),
I attempted to remove Demeter entirely and reinstall it from scratch. This
proved to be a serious mistake, as I presumably failed to completely purge
my system, and now cannot even get any installed programs to run at all.
Running ./Build Test produces lines upon lines of Dubious, test returned 2
(wstat 512, 0x200), and attempting to run dathena outputs this garbage:

Can't locate PerlIO/utf8_strict.pm in @INC (you may need to install the
> PerlIO::utf8_strict module) (@INC contains:
> /home/melville/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
> /home/melville/perl5/lib/perl5/5.22.1
> /home/melville/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
> /home/melville/perl5/lib/perl5 /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1
> /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5
> /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
> /usr/local/share/perl/5.22.1/Mixin/Linewise/Readers.pm line 9.
> BEGIN failed--compilation aborted at
> /usr/local/share/perl/5.22.1/Mixin/Linewise/Readers.pm line 9.
> Compilation failed in require at
> /usr/local/share/perl/5.22.1/Config/INI/Reader.pm line 5.
> BEGIN failed--compilation aborted at
> /usr/local/share/perl/5.22.1/Config/INI/Reader.pm line 5.
> Compilation failed in require at /usr/share/perl/5.22/parent.pm line 20.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/IniReader.pm line 2.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/Config.pm line 31.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/Config.pm line 31.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter.pm line 191.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter.pm line 191.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 24.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 24.
> Compilation failed in require at /usr/local/bin/dathena line 31.
> BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31.
> Use of uninitialized value $Larch::larch_exe in concatenation (.) or
> string at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Larch.pm line 288.
> Can't exec "-q": No such file or directory at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Larch.pm line 288.
>

I've attached a full error log from the build test, but I'm hardly
optimistic I can clean up my mess at this point. My current plan is to
create a 19.10 partition just to run Demeter. Such is the life of a
mediocre Linux user.

Thanks,
Jo Melville



On Wed, Nov 13, 2019 at 4:12 PM Jo Melville <melville at mit.edu> wrote:

> Hello all,
>
> I am having some troubles successfully building Demeter from source on my
> Linux machine. All dependencies appeared to install correctly -- a few
> errors pop up upon running ./Build test (full error report attached), but
> as best I could discern, the errors produced were the same as those
> reported in this recent message
> <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html>
> (
> https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html
> ).
>
> Athena appear to install correctly and even start correctly, but upon
> attempting to import *any* data file into Athena, the following error
> message pops up (screenshot also attached):
>
>
>> 03:50:59 PM: Unknown warnings category 'experimental::script_run' at
>> /usr/share/perl/5.22/warnings.pm line 254.
>> warnings::Croaker("Unknown warnings category 'experimental::script_run'")
>> called at /usr/share/perl/5.22/warnings.pm line 332
>> warnings::unimport("warnings", "experimental::script_run") called at
>> (eval 2455) line 1
>> Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> eval 'no warnings "experimental::script_run";
>>                           qr/(*script_run: ^ .* $ )/x' called at
>> /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74
>> require Pod/Simple/BlackBox.pm called at
>> /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7
>> Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Simple/LinkSection.pm called at
>> /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9
>> Pod::Simple::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34
>> Pod::Text::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Text.pm called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm
>> line 13
>> Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Demeter/UI/Athena/PluginRegistry.pm called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114
>> Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0),
>> "PluginRegistry") called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260
>> Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0),
>> "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called
>> at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line
>> 168
>> Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0))
>> called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm
>> line 890
>> Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570),
>> Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0))
>> called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm
>> line 808
>> Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570),
>> Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35
>> eval {...} called at /usr/local/bin/dathena line 35
>>
>> 03:50:59 PM: Unknown warnings category 'experimental::script_run' at
>> /usr/share/perl/5.22/warnings.pm line 254.
>> warnings::Croaker("Unknown warnings category 'experimental::script_run'")
>> called at /usr/share/perl/5.22/warnings.pm line 332
>> warnings::unimport("warnings", "experimental::script_run") called at
>> (eval 2455) line 1
>> Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> eval 'no warnings "experimental::script_run";
>>                           qr/(*script_run: ^ .* $ )/x' called at
>> /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74
>> require Pod/Simple/BlackBox.pm called at
>> /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7
>> Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Simple/LinkSection.pm called at
>> /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9
>> Pod::Simple::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34
>> Pod::Text::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Pod/Text.pm called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm
>> line 13
>> Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1
>> eval {...} called at (eval 2455) line 1
>> require Demeter/UI/Athena/PluginRegistry.pm called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114
>> Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0),
>> "PluginRegistry") called at
>> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260
>> Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0),
>> "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called
>> at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line
>> 168
>> Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0))
>> called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm
>> line 890
>> Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570),
>> Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0))
>> called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm
>> line 808
>> Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570),
>> Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35
>> eval {...} called at /usr/local/bin/dathena line 35
>> BEGIN failed--compilation aborted at (eval 2455) line 1.
>>
>
> Ignoring this message allows Athena to import data correctly at first, but
> clicking some buttons will consistently and immediately cause the program
> to close, without even an error message popping up. Actions that will
> induce a crash range from selecting any Energy value besides 1 in column
> selection to things as innocuous as clicking Help>Show Tip.
>
> As a result, though the program is (barely) usable, it is very unstable
> and prone to crashing without warning, causing frustrating data loss. I'm
> sure that this is due to some fault on my part during the installation
> process, and would welcome any guidance on how best to approach this issue.
>
> Thanks,
> Jo Melville
>
>
> --
> Jonathan "Jo" Melville <https://stuff.mit.edu/~melville/>
> PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-)
> Contact: (620)-842-8756
>
> *“People think of education as something they can finish.”*
>
> *--Isaac Asimov*
>
>

-- 
Jonathan "Jo" Melville <https://stuff.mit.edu/~melville/>
PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-)
Contact: (620)-842-8756

*“People think of education as something they can finish.”*

*--Isaac Asimov*
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NOTE: Forcing use of Ifeffit in testing.
t/000_ifeffit.t ......... ok
t/001_base.t ............ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 24/24 subtests 
t/002_types.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 580/580 subtests 
t/003_config.t .......... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 22/22 subtests 
t/004_data.t ............ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 61/61 subtests 
t/005_plot.t ............ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 17/17 subtests 
t/006_gds.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 28/28 subtests 
t/007_prj.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 22/22 subtests 
t/008_path.t ............ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 23/23 subtests 
t/009_fit.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 25/25 subtests 
t/010_feff.t ............ 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 33/33 subtests 
t/011_sp.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 25/25 subtests 
t/012_atoms.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 17/17 subtests 
t/013_spacegroups.t ..... ok
t/014_vpath.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 10/10 subtests 
t/015_sspath.t .......... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 20/20 subtests 
t/016_fspath.t .......... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 16/16 subtests 
t/017_structuralunit.t .. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/12 subtests 
t/018_multichannel.t .... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 10/10 subtests 
t/019_provenance.t ...... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 4/4 subtests 
t/020_indicator.t ....... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/12 subtests 
t/021_externalfeff.t .... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 9/9 subtests 
t/022_filetypes.t ....... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 39/39 subtests 
t/023_files.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 4/4 subtests 
t/024_graph.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 4/4 subtests 
t/025_lcf.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 14/14 subtests 
t/026_xes.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 11/11 subtests 
t/028_fpath.t ........... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/12 subtests 
t/029_threebody.t ....... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 9/9 subtests 
t/030_xdi.t ............. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 25/25 subtests 
t/031_quench.t .......... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 130/130 subtests 
t/032_miscellany.t ...... 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 71/71 subtests 
t/100_elam.t ............ ok
t/101_mcmaster.t ........ ok
t/102_chantler.t ........ ok
t/103_henke.t ........... ok
t/104_shaltout.t ........ ok
t/105_fluo.t ............ ok
t/500_checker.t ......... ok
t/501_dataBlock.t ....... ok
t/502_dictionary.t ...... ok
t/503_filter.t .......... ok
t/504_parser.t .......... ok
t/505_writer.t .......... ok

Test Summary Report
-------------------
t/001_base.t          (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 24 tests but ran 0.
t/002_types.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 580 tests but ran 0.
t/003_config.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/004_data.t          (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 61 tests but ran 0.
t/005_plot.t          (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 17 tests but ran 0.
t/006_gds.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 28 tests but ran 0.
t/007_prj.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/008_path.t          (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 23 tests but ran 0.
t/009_fit.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 25 tests but ran 0.
t/010_feff.t          (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 33 tests but ran 0.
t/011_sp.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 25 tests but ran 0.
t/012_atoms.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 17 tests but ran 0.
t/014_vpath.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 10 tests but ran 0.
t/015_sspath.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 20 tests but ran 0.
t/016_fspath.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 16 tests but ran 0.
t/017_structuralunit.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 12 tests but ran 0.
t/018_multichannel.t  (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 10 tests but ran 0.
t/019_provenance.t    (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 4 tests but ran 0.
t/020_indicator.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 12 tests but ran 0.
t/021_externalfeff.t  (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 9 tests but ran 0.
t/022_filetypes.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 39 tests but ran 0.
t/023_files.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 4 tests but ran 0.
t/024_graph.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 4 tests but ran 0.
t/025_lcf.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 14 tests but ran 0.
t/026_xes.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 11 tests but ran 0.
t/028_fpath.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 12 tests but ran 0.
t/029_threebody.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 9 tests but ran 0.
t/030_xdi.t           (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 25 tests but ran 0.
t/031_quench.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 130 tests but ran 0.
t/032_miscellany.t    (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 71 tests but ran 0.
Files=44, Tests=1382, 24 wallclock secs ( 0.21 usr  0.08 sys + 22.60 cusr  1.43 csys = 24.32 CPU)
Result: FAIL
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