[Ifeffit] Installing demeter from source on Yosemite?

Anders Glans paglans at lbl.gov
Thu Mar 19 16:42:53 CDT 2015


Thank you for your quick reply. The output from ./Build touch_wrapper is included below.

Thanks,
Anders


$ sudo ./Build touch_wrapper
Password:
touching src/ifeffit_wrap.c
Use of uninitialized value $pgplot_location in substitution (s///) at DemeterBuilder.pm line 191.
cc -I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE -c -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -Os -o src/ifeffit_wrap.o src/ifeffit_wrap.c
src/ifeffit_wrap.c:634:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:660:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:689:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:718:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:750:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:782:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:814:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:852:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:878:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:908:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:934:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:962:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:995:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1029:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1063:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1103:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1131:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1154:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1179:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1206:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1235:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1264:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1287:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1313:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1340:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1370:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1399:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1424:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1451:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1482:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1514:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
31 warnings generated.
src/ifeffit_wrap.c:634:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:660:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:689:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:718:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:750:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:782:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:814:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:852:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:878:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:908:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:934:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:962:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:995:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1029:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1063:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1103:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1131:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1154:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1179:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1206:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1235:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1264:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1287:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1313:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1340:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1370:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1399:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1424:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1451:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1482:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
src/ifeffit_wrap.c:1514:11: warning: format string is not a string literal
      (potentially insecure) [-Wformat-security]
    croak(_swigerr);
          ^~~~~~~~
31 warnings generated.
env LD_RUN_PATH=/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE cc -mmacosx-version-min=10.10 -arch x86_64 -arch i386 -bundle -undefined dynamic_lookup -fstack-protector -o src/Ifeffit.dylib src/ifeffit_wrap.o
Simple test for presence of gnuplot ---> found it!  Using gnuplot with the x11 terminal.
Building Demeter
Building Artemis User's Guide
Building Athena User's Guide
copying src/Ifeffit.so to /Users/Anders/perl/auto/Ifeffit/Ifeffit.so



> On Mar 19, 2015, at 14:29 PM, Bruce Ravel <bravel at bnl.gov> wrote:
> 
> 
> Can you show us what happens when you attempt to build the ifeffit wrapper?  This can be forced by doing
> 
>    ./Build touch_wrapper
> 
> I am suspicious that never got built correctly.
> 
> B
> 
> 
> On 03/19/2015 05:21 PM, Anders Glans wrote:
>> Dear all,
>> 
>> Has anybody succeeded with installing demeter from source on a Mac? I
>> have attempted to install demeter from source on OS X 10.10.2, but so
>> far without success.
>> 
>> I have followed the installation procedure for Installing source code at
>> http://bruceravel.github.io/demeter/pods/installation.pod.html, except I
>> installed pgplot from source instead of using the install script
>> provided through ifeffit. I don’t get any errors installing either
>> pgplot or ifeffit.
>> 
>> All dependencies for demeter should be met:
>> 
>> $ sudo perl ./Build.PL
>> Password:
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'Demeter' version '0.9.21'
>> 
>> If all dependencies are met, build and install Demeter by doing:
>> <snip>
>> 
>> The build seems to go fine:
>> 
>> $ sudo ./Build
>> Simple test for presence of gnuplot ---> found it!  Using gnuplot with
>> the x11 terminal.
>> Building Demeter
>> Building Artemis User's Guide
>> Building Athena User's Guide
>> 
>> But the tests fail miserably. Already before the actual testing starts,
>> there is a message that loading of Ifeffit.bundle fails:
>> 
>> $ sudo ./Build test
>> t/000_ifeffit.t ......... Can't load
>> '/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle'
>> for module Ifeffit:
>> dlopen(/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle,
>> 2): Symbol not found: _ifeffit
>>   Referenced from:
>> /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
>>   Expected in: flat namespace
>>  in
>> /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle at
>> /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194.
>>  at t/000_ifeffit.t line 9.
>> Compilation failed in require at t/000_ifeffit.t line 9.
>> BEGIN failed--compilation aborted at t/000_ifeffit.t line 12.
>> # Looks like your test exited with 255 before it could output anything.
>> t/000_ifeffit.t ......... Dubious, test returned 255 (wstat 65280, 0xff00)
>> Failed 6/6 subtests
>> <snip>
>> 
>> 
>> However, the bundle exists:
>> $ ls -l /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/
>> total 152
>> -r-xr-xr-x  1 root  wheel  76208 Mar 18 13:09 Ifeffit.bundle
>> 
>> and the symbol in question is part of the bundle (well, at least the
>> string exists):
>> 
>> $ grep _ifeffit /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/*
>> Binary file
>> /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle matches
>> 
>> Does anybody know what is going on? Am I missing something?
>> 
>> A couple of more bits of information:
>> 
>> $ which ifeffit
>> /usr/local/bin/ifeffit
>> 
>> $ ifeffit
>>  Ifeffit   1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
>>                 command-line shell version 1.1 with GNU Readline
>> Ifeffit> testplot
>>  %PGPLOT, Unrecognized device type
>>  %PGPLOT, Invalid device specification: /AQT
>>  %PGPLOT, PGBBUF: selected graphics device is not open
>>  %PGPLOT, PGQCI: selected graphics device is not open
>>  %PGPLOT, PGQFS: selected graphics device is not open
>>  %PGPLOT, PGSCI: selected graphics device is not open
>>  %PGPLOT, PGSFS: selected graphics device is not open
>>  %PGPLOT, PGSVP: selected graphics device is not open
>>  %PGPLOT, PGBBUF: selected graphics device is not open
>>  %PGPLOT, PGEBUF: selected graphics device is not open
>>  %PGPLOT, PGSVP: selected graphics device is not open
>>  %PGPLOT, PGSCI: selected graphics device is not open
>>  %PGPLOT, PGSFS: selected graphics device is not open
>>  %PGPLOT, PGEBUF: selected graphics device is not open
>>   ** plot error: cannot open device:
>>  %PGPLOT, Unrecognized device type
>>  %PGPLOT, Invalid device specification: /AQT
>>   ** plot error: cannot open device:
>> Ifeffit> exit
>> 
>> $ which athena
>> /usr/local/bin/athena
>> 
>> $ athena
>> dyld: lazy symbol binding failed: Symbol not found: _iff_exec
>>   Referenced from:
>> /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
>>   Expected in: flat namespace
>> 
>> dyld: Symbol not found: _iff_exec
>>   Referenced from:
>> /Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
>>   Expected in: flat namespace
>> 
>> Trace/BPT trap: 5
>> 
>> 
>> 
>> Regards,
>> Anders
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
> 
> 
> -- 
> Bruce Ravel  ------------------------------------ bravel at 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/
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit





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