Problem running ATSAS programs on Mac os x el capitan

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SDKnight
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Problem running ATSAS programs on Mac os x el capitan

#1 Post by SDKnight » 2015.10.10 17:32

Hello,

I'm new to SAXS and to ATSAS but now have some SAXS data collected at BM29 at the ESRF that I want to continue to work with at home. I've installed ATSAS on my mac running Mac OS X El Capitan (10.11) but when I try to run primus it fails with the following error message:

dyld: Library not loaded: QtXmlPatterns.framework/Versions/4/QtXmlPatterns
Referenced from: /Applications/ATSAS/bin/primus.bin
Reason: image not found
Trace/BPT trap


Any advice on how to solve this will be much appreciated!

franke
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Re: Problem running ATSAS programs on Mac os x el capitan

#2 Post by franke » 2015.10.10 22:28

Oh blast. Seems you found yet another Mac packaging error. I'm looking into it. Thanks for the report.

SDKnight
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Re: Problem running ATSAS programs on Mac os x el capitan

#3 Post by SDKnight » 2015.10.13 09:32

Thanks for looking into this issue. Not sure if it will help you localise the problem, but I can install all versions up to and including 6.0, i.e. all versions installed from an installer on a disk image work, but the versions delivered as a compressed folder don't.

key
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Re: Problem running ATSAS programs on Mac os x el capitan

#4 Post by key » 2015.10.13 23:38

SDKnight wrote: dyld: Library not loaded: QtXmlPatterns.framework/Versions/4/QtXmlPatterns
Referenced from: /Applications/ATSAS/bin/primus.bin
Reason: image not found
Trace/BPT trap
I can also confirm the issue here on MacOSX 10.8 - 10.10
It appears primus.bin, sasplot.bin, sasdoc.bin, and gnomplot.bin have incorrect library paths or are missing Frameworks in their .app bundles

Thanks for looking into it.

Cheers,
Jason

franke
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Re: Problem running ATSAS programs on Mac os x el capitan

#5 Post by franke » 2015.10.28 21:27

Please try ATSAS-2.7.1. The issues we had with the Mac packages should have been resolved there.

rlkingston
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Re: Problem running ATSAS programs on Mac os x el capitan

#6 Post by rlkingston » 2015.11.02 05:52

With the 2.7.1 release, I'm still seeing the same error under OS X 10.11. This is what I get if I try and launch the Apps.

Dyld Error Message:
Library not loaded: QtXmlPatterns.framework/Versions/4/QtXmlPatterns
Referenced from: /Applications/ATSAS/gnomplot.app/Contents/MacOS/gnomplot
Reason: no suitable image found. Did find:
/Library/Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns: no matching architecture in universal wrapper


Best Regards,

Richard

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Re: Problem running ATSAS programs on Mac os x el capitan

#7 Post by franke » 2015.11.02 10:31

rlkingston wrote:With the 2.7.1 release, I'm still seeing the same error under OS X 10.11.
Dyld Error Message:
Library not loaded: QtXmlPatterns.framework/Versions/4/QtXmlPatterns
Richard, could you please verify that indeed you installed 2.7.1? This issue has been reported fixed in another thread. Could you please try to determine the revision of the binaries installed as shown there? Thanks.

rlkingston
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Re: Problem running ATSAS programs on Mac os x el capitan

#8 Post by rlkingston » 2015.11.02 11:12

I looked at this at the end of a long day. In fact I looked at the wrong binaries (Best not to ask how).

The 2.7.1 versions are indeed working fine. So sorry about that & thanks for fixing this so promptly.

Richard

dlogan
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Re: Problem running ATSAS programs on Mac os x el capitan

#9 Post by dlogan » 2015.11.26 17:03

Hi,

I am having an installation problem almost identical to the one described here, but subtly different. I have installed ATSAS 2.7.1 for OS X 10.10 and I am running 10.11 (where I have seen that others have got it to work!) However when I try to run any GUI program I get the following:

Code: Select all

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
 Library not loaded: /usr/local/lib/QtSvg.framework/Versions/4/QtSvg
 Referenced from: /Applications/ATSAS/primus.app/Contents/MacOS/primus
 Reason: image not found
Why is my system looking for the run time libraries in /usr/local/lib and not in the ATSAS directory? I have checked my DYLD_LIBRARY_PATH variable in a terminal window and it doesn't appear to be set. I tried setting it to /Applications/ATSAS/lib and running e.g. primus from the command line but it still looks in /usr/local/lib. Any tips?

atuckwell
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Re: Problem running ATSAS programs on Mac os x el capitan

#10 Post by atuckwell » 2015.11.28 13:59

Hello,

I am also having issues with ATSAS 2.7.1 on El Capitan (OSX 10.11). None of the GUI programs will run, displaying a similar error

Code: Select all

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
  Library not loaded: /Applications/ATSAS/lib/libsaxsplot.dylib
  Referenced from: /Applications/ATSAS-2.7.1/gnomplot.app/Contents/MacOS/gnomplot
  Reason: image not found
However, this is the correct path. libsaxplot.dylib is there:

Code: Select all

Andrews-MBP:lib andrewtuckwell$ pwd
/Applications/ATSAS-2.7.1/lib
Andrews-MBP:lib andrewtuckwell$ ls
libQtCLucene.4.8.6.dylib	        libgfortran.3.dylib
libQtCore.4.8.6.dylib		libquadmath.0.dylib
libQtGui.4.8.6.dylib		        libqwt.5.2.0.dylib
libQtHelp.4.8.6.dylib		libqwt.dylib
libQtNetwork.4.8.6.dylib	        libsaxsdocument.1.dylib
libQtSql.4.8.6.dylib		        libsaxsdocument.dylib
libQtSvg.4.8.6.dylib		        libsaxsplot.dylib
libQtWebKit.4.8.6.dylib		libstdc++.6.dylib
libQtXml.4.8.6.dylib		        plugins
libQtXmlPatterns.4.8.6.dylib	python2.7
libgcc_s.1.dylib
Any advice here? Have others managed to get ATSAS up on El Capitan?


NOTE: I noticed immediately after posting that the path listed in the original error was : /Applications/ATSAS/lib/libsaxsplot.dylib rather than /Applications/ATSAS-2.7.1/lib/libsaxsplot.dylib
Changing the directory name to just "ATSAS" and running gnomplot gave and altered error:

Code: Select all

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
  Library not loaded: /usr/local/lib/QtSvg.framework/Versions/4/QtSvg
  Referenced from: /Applications/ATSAS/gnomplot.app/Contents/MacOS/gnomplot
  Reason: image not found
This path does not exist:

Code: Select all

ANDREWS-MBP:local andrewtuckwell$ pwd
/usr/local
ANDREWS-MBP:local andrewtuckwell$ ls -la
total 0
Out of my depth here!

franke
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Re: Problem running ATSAS programs on Mac os x el capitan

#11 Post by franke » 2015.11.28 20:50

First up to the users of 10.11: we do not have an installation of 10.11 we could test on. Our IT discouraged updates because of various incompatibilities elsewhere. In other words, I would not be surprised if it would not work. However, the path issues should not be there, one way or another. All the required non-system libraries are included in the .tar.gz and all the library paths (should) have been fixed up. Above a user of 10.10 confirmed it fixed.

Now. Did you install to "/Applications/ATSAS" and nowhere else? In case you have "otool" available (part of xcode), what does "otool -L" of the binary in question give you? It should only show system libraries and stuff that is expected in /Applications/ATSAS/lib, nothing, absolutely nothing is, or better, should be, searched for in /usr/local. Like here for primus (gnomplot would give essentially the same output):

Code: Select all

$ pwd
/Applications/ATSAS
$ otool -L primus.app/Contents/MacOS/primus 
primus.app/Contents/MacOS/primus:
        /Applications/ATSAS/lib/libsaxsplot.dylib (compatibility version 0.0.0, current version 0.0.0)
        /Applications/ATSAS/lib/libsaxsdocument.1.dylib (compatibility version 0.0.0, current version 1.0.0)
        /Applications/ATSAS/lib/libqwt.5.2.0.dylib (compatibility version 0.0.0, current version 5.2.0)
        /Applications/ATSAS/lib/libQtSvg.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libQtXmlPatterns.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libQtGui.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libQtXml.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libQtNetwork.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libQtCore.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
        /Applications/ATSAS/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

atuckwell
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Re: Problem running ATSAS programs on Mac os x el capitan

#12 Post by atuckwell » 2015.11.30 02:29

Thanks Franke, I knew there would be a bit of a risk that things would be slow to get going with such a new OS release.
Still I think there may be an issue problem with the paths..

This is the otool output for the primus binary contained in atsas-2.7.1-1-OSX-10.10.x86_64.tar release

Code: Select all

Andrews-MBP:ATSAS andrewtuckwell$ pwd
/Applications/ATSAS
Andrews-MBP:ATSAS andrewtuckwell$ otool -L primus.app/Contents/MacOS/primus
primus.app/Contents/MacOS/primus:
	/Applications/ATSAS/lib/libsaxsplot.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Applications/ATSAS/lib/libqwt.5.2.0.dylib (compatibility version 0.0.0, current version 5.2.0)
	/usr/local/lib/QtSvg.framework/Versions/4/QtSvg (compatibility version 4.8.0, current version 4.8.6)
	/usr/local/lib/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.6)
	/usr/local/lib/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.6)
	/usr/local/lib/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.6)
	/usr/local/lib/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.6)
	/usr/local/lib/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libsaxsdocument.1.dylib (compatibility version 0.0.0, current version 1.0.0)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/Applications/ATSAS/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
And this is the otool output for the primus binary contained in the atsas-2.7.1-1-OSX-10.9.x86_64.tar release

Code: Select all

Andrews-MacBook-Pro:ATSAS andrewtuckwell$ pwd
/Applications/ATSAS
Andrews-MacBook-Pro:ATSAS andrewtuckwell$ otool -L primus.app/Contents/MacOS/primus
primus.app/Contents/MacOS/primus:
	/Applications/ATSAS/lib/libsaxsplot.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Applications/ATSAS/lib/libsaxsdocument.1.dylib (compatibility version 0.0.0, current version 1.0.0)
	/Applications/ATSAS/lib/libqwt.5.2.0.dylib (compatibility version 0.0.0, current version 5.2.0)
	/Applications/ATSAS/lib/libQtSvg.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libQtXmlPatterns.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libQtGui.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libQtXml.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libQtNetwork.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/Applications/ATSAS/lib/libQtCore.4.8.6.dylib (compatibility version 4.8.0, current version 4.8.6)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/Applications/ATSAS/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
In anycase this 2.7.1 for OSX10.9 release is working for me on El Capitan.

One of my colleagues mentioned that they had a similar issue with versions on Yosemite (that OSX10.10 release didn't work but the OSX10.9 did) but haven't confirmed this.

dlogan
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Re: Problem running ATSAS programs on Mac os x el capitan

#13 Post by dlogan » 2015.12.15 20:33

Sorry for not following up on this earlier. Teaching duties :roll:
The solution of using the 10.9 build works for me. Thanks for this suggestion. I actually thought I had tried it already but apparently not!

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