Re: [Ifeffit] Installing demeter from source on Yosemite?

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 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

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-- 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/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit