Trouble installing demeter on Mint 17.1
Dear list, After upgrading my Linux OS to Mint 17.1, I have trouble installing demeter again (on Mint 14 it used to install and run without problems). sudo ./Build installdeps failed to install a few dependencies even after issuing the command several times (Wx and Regexp:Assemble), so I installed them manually from the Mint repositories. After that, perl ./Build.PL said that all dependencies were satisfied. I then ran ./Build which finished, I think, normally. The only lines that look remotely suspicious are: Chantler data conversion tool 1.2 for Absorption 0.10 Parsing lines ... Parsing element 5Argument "8.20144-01" isn't numeric in numeric le (<=) at lib/Xray/data/chantler2st.PL line 120, <CHANTLER> line 81. 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Getting energy list keys ... sorting energy list ... and making energy hash Saving new database, lib/Xray/data/../Absorption/chantler.db. However, when I run ./Build test it shows that 2/44 tests fail (5/2681 subtests). Please find the terminal output below. It might be usefull to mention that at first I tried to install demeter without root privileges (following the Dave Hughes' guide), with same tests failing. I went on to ./Build install anyway, and it succeded, but when trying to open previously saved projects, dathena would crash. I then removed demeter and the local perl directory, and tried installing demeter again, this time with root privileges following Bruce Ravel's guide. Any help would be appreciated, thank you in advance! ./Build test terminal output: t/000_ifeffit.t ......... ok t/001_base.t ............ ok t/002_types.t ........... ok # Failed test 'configuration system introspection works: groups 37 artemis' # at t/003_config.t line 61. # Failed test 'configuration system introspection works: main_groups 37' # at t/003_config.t line 63. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 74. # Failed test 'introspection after reading new group: main_groups' # at t/003_config.t line 76. # Looks like you failed 4 tests of 24. t/003_config.t .......... Failed 4/24 subtests t/004_data.t ............ ok t/005_plot.t ............ ok t/006_gds.t ............. ok t/007_prj.t ............. ok t/008_path.t ............ ok # Failed test 'statistics reporting seems ok' # at t/009_fit.t line 97. # Looks like you failed 1 test of 25. t/009_fit.t ............. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/25 subtests t/010_feff.t ............ ok t/011_sp.t .............. ok t/012_atoms.t ........... ok t/013_spacegroups.t ..... ok t/014_vpath.t ........... ok t/015_sspath.t .......... ok t/016_fspath.t .......... ok t/017_structuralunit.t .. ok t/018_multichannel.t .... ok t/019_provenance.t ...... ok t/020_indicator.t ....... ok t/021_externalfeff.t .... ok t/022_filetypes.t ....... ok t/023_files.t ........... ok t/024_graph.t ........... ok t/025_lcf.t ............. ok t/026_xes.t ............. ok t/028_fpath.t ........... ok t/029_threebody.t ....... ok t/030_xdi.t ............. ok t/031_quench.t .......... ok t/032_miscellany.t ...... ok 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/003_config.t (Wstat: 0 Tests: 24 Failed: 4) Failed tests: 17-18, 23-24 t/009_fit.t (Wstat: 256 Tests: 25 Failed: 1) Failed test: 17 Non-zero exit status: 1 Files=44, Tests=2681, 69 wallclock secs ( 0.29 usr 0.06 sys + 67.36 cusr 2.64 csys = 70.35 CPU) Result: FAIL Failed 2/44 test programs. 5/2681 subtests failed. Kind regards, Stevan Ognjanovic -- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic@uni-due.de
Hi Stevan, The errors during ./Build and ./Build test were both pretty innocuous and easily fixed. I just pushed solutions to the github repo. Thanks for noticing and reporting those. The major problem you report is that athena was crashing. It would be helpful to tell me what gets written to the terminal when this happens. That said, I suspect this is because you /updated/ Mint and Demeter's build script failed to recognize that the Ifeffit wrapper needed to be recompiled for an updated version of perl. When you do "perl Build.PL", it says this, among other things: If you are reinstalling Demeter after updating your operating system (or updating perl), you may need to do: ./Build touch_wrapper ./Build test ./Build install (or sudo ./Build install) That is trying to prompt you about the problem I suspect you are seeing. What happens if you do "./Build touch_wrapper", as suggested? Does athena then run? Cheers, B On 02/18/2015 04:21 AM, Stevan Ognjanovic wrote:
After upgrading my Linux OS to Mint 17.1, I have trouble installing demeter again (on Mint 14 it used to install and run without problems). sudo ./Build installdeps failed to install a few dependencies even after issuing the command several times (Wx and Regexp:Assemble), so I installed them manually from the Mint repositories. After that, perl ./Build.PL said that all dependencies were satisfied. I then ran ./Build which finished, I think, normally. The only lines that look remotely suspicious are:
Chantler data conversion tool 1.2 for Absorption 0.10 Parsing lines ... Parsing element 5Argument "8.20144-01" isn't numeric in numeric le (<=) at lib/Xray/data/chantler2st.PL line 120, <CHANTLER> line 81. 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Getting energy list keys ... sorting energy list ... and making energy hash Saving new database, lib/Xray/data/../Absorption/chantler.db.
However, when I run ./Build test it shows that 2/44 tests fail (5/2681 subtests). Please find the terminal output below.
It might be usefull to mention that at first I tried to install demeter without root privileges (following the Dave Hughes' guide), with same tests failing. I went on to ./Build install anyway, and it succeded, but when trying to open previously saved projects, dathena would crash. I then removed demeter and the local perl directory, and tried installing demeter again, this time with root privileges following Bruce Ravel's guide.
Any help would be appreciated, thank you in advance!
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, First of all, thank you for your response. I did not update Mint, I installed a fresh version (formated the drive, installed a new version, remounted my data partitions, including the home folder, and reinstalled all the packages from the repositories), sorry if I did not make it clear enough in the first email. The demeter folder in the home folder was carried over from the old linux version, but I downloaded the newest version from the github repo. I would think this is basically equal to starting with a blank OS. Anyway, I did try the ./Build touch_wrapper command without any success (same tests failed if I remember correctly). As you asked me about athena crashing, for the purpose of testing it, I went on and installed athena despite the errors in the ./Build test command (without downloading the new version from the github repo). This is the terminal output: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 0,34568900723742 at accessor Demeter::Data::bkg_nc0 (defined at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 310) line 4 Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xcf3fd70)', '0,34568900723742') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 717 Demeter::Data::_update('Demeter::Data=HASH(0xcf3fd70)', 'fft') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 Demeter::Data::Plot::plot('Demeter::Data=HASH(0xcf3fd70)', 'E') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 2177 Demeter::UI::Athena::plot('Demeter::UI::Athena=HASH(0x1a65618)', '', '', 'E', 'single') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 2376 Demeter::UI::Athena::quadplot('Demeter::UI::Athena=HASH(0x1a65618)', 'Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 238 Demeter::UI::Athena::IO::Import_plot('Demeter::UI::Athena=HASH(0x1a65618)', 'Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 813 Demeter::UI::Athena::IO::_prj('Demeter::UI::Athena=HASH(0x1a65618)', '/home/stevan/Documents/.../athenaprojectname.prj', '/home/stevan/Documents/.../athenaprojectname.prj', 1, '') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0x1a65618)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 857 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x19a2980)', 'Wx::CommandEvent=SCALAR(0xcf2b6d0)', 'Demeter::UI::Athena=HASH(0x1a65618)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 780 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x19a2980)', 'Wx::CommandEvent=SCALAR(0xcf2b6d0)') called at /home/stevan/perl5/bin/dathena line 39 eval {...} at /home/stevan/perl5/bin/dathena line 39 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- After removing demeter and perl5 folders from the home directory, downloading the latest packages from the github repo and building from scratch, all test were successful in the ./Build test step. Demeter installed without problems. But, athena still crashes when I try to open a project or import any data. This is the terminal output (this time after trying to import data in .dat format): ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Attribute (bkg_e0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 1582,00000 at accessor Demeter::Data::bkg_e0 (defined at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 226) line 7 Demeter::Data::bkg_e0('Demeter::Data=HASH(0xe5ca148)', '1582,00000') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/E0.pm line 67 Demeter::Data::E0::e0_ifeffit('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/E0.pm line 37 Demeter::Data::E0::e0('Demeter::Data=HASH(0xe5ca148)', 'ifeffit') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 289 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 732 Demeter::Data::_update('Demeter::Data=HASH(0xe5ca148)', 'all') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 603 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0x1d0d640)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xe602810)', 'Demeter::Data=HASH(0xe5ca148)', 'HASH(0xe5c5f08)', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', 0, 0) called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 486 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0x1d0d640)', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', 1, 0) called at /home/stevan/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(0x1d0d640)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 857 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x1c77980)', 'Wx::CommandEvent=SCALAR(0xd200dd0)', 'Demeter::UI::Athena=HASH(0x1d0d640)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 780 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x1c77980)', 'Wx::CommandEvent=SCALAR(0xd200dd0)') called at /home/stevan/perl5/bin/dathena line 39 eval {...} at /home/stevan/perl5/bin/dathena line 39 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Doing ./Build touch_wrapper does not change anything - all tests pass, demeter installs, but athena crashes again... Looking forward to your reply and suggestions on how to solve this problem. Kind regards, Stevan -- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic@uni-due.de
Stevan, Could you read this thread: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04371.htm... The vacation-related parts -- no so relevant :) The localization-related parts are relevant. You'll notice that Denis asked about the exact same error message. The latter half of http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04374.htm... has all of the same suggestions I want to make now. The reply to that post suggested that it was solvable. If you are uncomfortable resetting those environment variables system-wide, I have some ideas for how to set them gracefully for each instance of Athena or Artemis. Let me know if you want to pursue that. B On 02/18/2015 12:43 PM, Stevan Ognjanovic wrote:
Dear Bruce,
First of all, thank you for your response.
I did not update Mint, I installed a fresh version (formated the drive, installed a new version, remounted my data partitions, including the home folder, and reinstalled all the packages from the repositories), sorry if I did not make it clear enough in the first email. The demeter folder in the home folder was carried over from the old linux version, but I downloaded the newest version from the github repo. I would think this is basically equal to starting with a blank OS. Anyway, I did try the ./Build touch_wrapper command without any success (same tests failed if I remember correctly).
As you asked me about athena crashing, for the purpose of testing it, I went on and installed athena despite the errors in the ./Build test command (without downloading the new version from the github repo). This is the terminal output:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 0,34568900723742 at accessor Demeter::Data::bkg_nc0 (defined at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 310) line 4 Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xcf3fd70)', '0,34568900723742') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 717 Demeter::Data::_update('Demeter::Data=HASH(0xcf3fd70)', 'fft') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 Demeter::Data::Plot::plot('Demeter::Data=HASH(0xcf3fd70)', 'E') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 2177 Demeter::UI::Athena::plot('Demeter::UI::Athena=HASH(0x1a65618)', '', '', 'E', 'single') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 2376 Demeter::UI::Athena::quadplot('Demeter::UI::Athena=HASH(0x1a65618)', 'Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 238 Demeter::UI::Athena::IO::Import_plot('Demeter::UI::Athena=HASH(0x1a65618)', 'Demeter::Data=HASH(0xcf3fd70)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 813 Demeter::UI::Athena::IO::_prj('Demeter::UI::Athena=HASH(0x1a65618)', '/home/stevan/Documents/.../athenaprojectname.prj', '/home/stevan/Documents/.../athenaprojectname.prj', 1, '') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0x1a65618)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 857 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x19a2980)', 'Wx::CommandEvent=SCALAR(0xcf2b6d0)', 'Demeter::UI::Athena=HASH(0x1a65618)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 780 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x19a2980)', 'Wx::CommandEvent=SCALAR(0xcf2b6d0)') called at /home/stevan/perl5/bin/dathena line 39 eval {...} at /home/stevan/perl5/bin/dathena line 39
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
After removing demeter and perl5 folders from the home directory, downloading the latest packages from the github repo and building from scratch, all test were successful in the ./Build test step. Demeter installed without problems. But, athena still crashes when I try to open a project or import any data. This is the terminal output (this time after trying to import data in .dat format):
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Attribute (bkg_e0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 1582,00000 at accessor Demeter::Data::bkg_e0 (defined at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 226) line 7 Demeter::Data::bkg_e0('Demeter::Data=HASH(0xe5ca148)', '1582,00000') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/E0.pm line 67 Demeter::Data::E0::e0_ifeffit('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/E0.pm line 37 Demeter::Data::E0::e0('Demeter::Data=HASH(0xe5ca148)', 'ifeffit') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 289 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xe5ca148)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 732 Demeter::Data::_update('Demeter::Data=HASH(0xe5ca148)', 'all') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 603 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0x1d0d640)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xe602810)', 'Demeter::Data=HASH(0xe5ca148)', 'HASH(0xe5c5f08)', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', 0, 0) called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 486 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0x1d0d640)', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', '/home/stevan/Documents/Project/Samples/XAFS/Samples-Canada/SO-58/Al-K/SO-58-XAS_1.dat', 1, 0) called at /home/stevan/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(0x1d0d640)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 857 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x1c77980)', 'Wx::CommandEvent=SCALAR(0xd200dd0)', 'Demeter::UI::Athena=HASH(0x1d0d640)') called at /home/stevan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 780 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x1c77980)', 'Wx::CommandEvent=SCALAR(0xd200dd0)') called at /home/stevan/perl5/bin/dathena line 39 eval {...} at /home/stevan/perl5/bin/dathena line 39
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Doing ./Build touch_wrapper does not change anything - all tests pass, demeter installs, but athena crashes again...
Looking forward to your reply and suggestions on how to solve this problem.
Kind regards, Stevan
-- Stevan Ognjanovic, Dipl.-Ing.
Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg
Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web:www.nppt.de e-mail:stevan.ognjanovic@uni-due.de
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 02/18/2015 12:43 PM, Stevan Ognjanovic wrote:
I did not update Mint, I installed a fresh version (formated the drive, installed a new version, remounted my data partitions, including the home folder, and reinstalled all the packages from the repositories), sorry if I did not make it clear enough in the first email. The demeter folder in the home folder was carried over from the old linux version, but I downloaded the newest version from the github repo. I would think this is basically equal to starting with a blank OS. Anyway, I did try the ./Build touch_wrapper command without any success (same tests failed if I remember correctly).
Still not 100% clear what your situation is. But this: The demeter folder in the home folder was carried over from the old linux version, suggests that you might be running into a problem with binary compatibility of the ifeffit wrapper with the new version of perl. But it's hard to tell. I discuss this in one of my posts in the thread I pointed you to in my last email. Also, I don't know what you mean by "downloaded the newest version from the github repo". You won't see something I pushed to the head of the master branch unless you do a "git pull". If you follow one of the download links, those just point to the most recently tagged release, which only gets updated when I tag a new release. If you clone or pull from the head of the master branch, you will find that the mistakes in the test scripts are fixed. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Dear Bruce, Denis Thank you for the quick (and simple, once you know what to look for) solution - it was indeed a locale problem. I managed to sort it out, I don't mind setting the LC_Numeric to en_US system-wide (it's something I wanted to do anyway), but now I'm getting other locale errors and warnings whenever I start a new terminal session. Anyway, this is not a demeter issue, so I won't be bothering you with it. As for the installation, when I wrote I downloaded from the github repo, what I meant was I issued the following command in terminal: git clone https://github.com/bruceravel/demeter.git That's why it worked without the errors in the ./Build test step this time. Once again, thanks for your help! Kind regards, Stevan Ognjanovic -- Stevan Ognjanovic, Dipl.-Ing. Nanoparticle Process Technology Department of Engineering Sciences University Duisburg-Essen Lotharstraße 1, MA 349 D-47057 Duisburg Phone: +49 (0)203 379 1783 Mobile phone: +49 (0)157 3820 6890 Fax: +49 (0)203 379 4453 web: www.nppt.de e-mail: stevan.ognjanovic@uni-due.de
On 02/19/2015 06:45 AM, Stevan Ognjanovic wrote:
Thank you for the quick (and simple, once you know what to look for) solution - it was indeed a locale problem. I managed to sort it out, I don't mind setting the LC_Numeric to en_US system-wide (it's something I wanted to do anyway), but now I'm getting other locale errors and warnings whenever I start a new terminal session. Anyway, this is not a demeter issue, so I won't be bothering you with it.
Hi Stevan, Glad it all worked out. Changing localization variables can have surprising consequences. (It was kind of surprising how Athena reacted!) If you are not comfortable simply setting something like LANG to en_US, you can make an alias that starts Athena within an altered environment. Following Denis' suggestion, you could put something like this in your .bashrc file (or the equivalent if you use another shell): alias athena='(export LANG=en_US/UTF-8 && /usr/local/bin/athena)' That will leave LANG untouched in the shell, but run Athena in a way that will not trigger the issue that started this conversation. That's bash syntax, it may be a bit different in another shell. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (2)
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Bruce Ravel -
Stevan Ognjanovic