[slicer-users] problem starting with OSX 10.5.8

Aryeh Weiss aryeh at cc.huji.ac.il
Thu Sep 30 17:03:09 EDT 2010



I think I got it. It seems that all over the lib directories, I have 
things like this:

-rwxr-xr-x   1 amw  staff    84300 Aug  4 02:23 libvtkzlib.5.6.0.dylib
-rwxr-xr-x   1 amw  staff        0 Aug 20 18:52 libvtkzlib.5.6.dylib
-rwxr-xr-x   1 amw  staff        0 Aug 20 18:52 libvtkzlib.dylib
-

Then, when I launch Slicer3, I get the following:

dyld: Library not loaded: libvtkzlib.5.6.dylib
   Referenced from: 
/Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
   Reason: no suitable image found.  Did find:
	/Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/lib/vtk-5.6/libvtkzlib.5.6.dylib: unknown file type, first eight bytes: 0x00 0x00 0x00 0x00 0x98 0x83 0xFF 0xBF

Note that it is a different dylib this time, and it is the zero length 
file that is referenced, and which then fails.

At first it was files in Insight, where the zero length files were 3.18 
and the nonzero length files were 3.18.0 . So I renamed all the 3.18.0 
files to 3.18, and then the error occurred in a different dylib 
directory.  After two rounds of this, I gave up trying to manually do this.

I think that the original intention might have been to link the 
"generic" names to the subversion specific names. Anyway, if this can be 
done in the release, it will be a lot easier than for me to keep 
launching the app, see where it fails , link or rename, and then iterate 
-- there are a lot of dylib directories.

--aryeh

On 9/30/10 10:11 PM, Steve Pieper wrote:
> Hi Aryeh -
>
> I think that's a red herring - /Users/hayes refers to the original build
> directory, but it's clear from your error messages that is it finding
> the distribution version of that file, in your Desktop folder. It's just
> that the installation appears to have gotten corrupted for some unknown
> reason.
>
>
> Googling for "mac dylib unknown file type, first eight bytes" turns up
> lots of error reports about similar issues, but no real solutions that I
> could see... It's a mystery to me.
>
> -Steve
>
> On 09/30/2010 03:28 PM, Aryeh Weiss wrote:
>> Hi Steve,
>>
>> Before I give up, I have one question that may relate to my inability to
>> run slicer. In the error test, there is a line:
>>
>> dyld: Library not loaded:
>> /Users/hayes/Slicer-3-6/Slicer3-lib/Insight-build/bin/libITKFEM.3.18.dylib
>>
>> Referenced from:
>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
>>
>> Why is there a reference to /Users/hayes/....
>> I have no such user on my system -- is this path buried somewhere in
>> Slicer?
>>
>> Best regards
>> --aryeh
>>
>> On 9/28/10 10:20 PM, Steve Pieper wrote:
>>> Hi Aryeh -
>>>
>>> Here's a copy of the file that you can try downloading:
>>>
>>>> http://dl.dropbox.com/u/1686930/libITKFEM.3.18.0.dylib
>>>
>>> Save it in place of this file that the error message complains about:
>>>
>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/lib/InsightToolkit/libITKFEM.3.18.dylib
>>>
>>>
>>>
>>>
>>> Regarding which other version might work, I can't say for sure. If the
>>> replacement lib doesn't work, I think maybe we'll need to figure out why
>>> your directory ends up differently after the archive is unpacked.
>>>
>>> HTH,
>>> Steve
>>>
>>> On 09/28/2010 12:58 PM, Aryeh Weiss wrote:
>>>> I already tried "falling back" to one version previous, without
>>>> success.
>>>> It would be awkward to keep trying previous versions one by one, but if
>>>> you have a particular version to suggest, I will be happy to try it.
>>>>
>>>> Alternatively, perhaps you can send me a known good file, and tell me
>>>> where to place it. If the error is unchanged, then we know something is
>>>> wrong with the search path to this file, and there is a similarly named
>>>> file buried somewhere else.
>>>>
>>>> --aryeh
>>>>
>>>> On 9/28/10 4:26 PM, Steve Pieper wrote:
>>>>> That is very curious - sorry you are having trouble. The report of the
>>>>> first 8 bytes of the file does not match the version I extracted. We
>>>>> could dig in more on that file, but maybe another idea would be to
>>>>> test
>>>>> if a different version of slicer works on your machine?
>>>>>
>>>>> -Steve
>>>>>
>>>>> On 09/28/2010 09:31 AM, Aryeh Weiss wrote:
>>>>>> Thanks again for your reply.
>>>>>>
>>>>>> I downloaded again and extracted.
>>>>>>
>>>>>> Same problem -- here is the output:
>>>>>>
>>>>>> Slicer3-3.6.1-2010-08-20-darwin-x86 amw$ ./Slicer3
>>>>>> Setting up launch environment...
>>>>>> dyld: Library not loaded:
>>>>>> /Users/hayes/Slicer-3-6/Slicer3-lib/Insight-build/bin/libITKFEM.3.18.dylib
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Referenced from:
>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
>>>>>>
>>>>>>
>>>>>> Reason: no suitable image found. Did find:
>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/lib/InsightToolkit/libITKFEM.3.18.dylib:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> unknown file type, first eight bytes: 0x00 0x00 0x00 0x00 0xA4 0x87
>>>>>> 0xFF
>>>>>> 0xBF
>>>>>>
>>>>>> Launch
>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
>>>>>>
>>>>>>
>>>>>> returned with error: child killed: trace trap
>>>>>>
>>>>>> CHILDKILLED 17052 SIGTRAP {trace trap}
>>>>>> _X11TransSocketINETConnect() can't get address for
>>>>>> /tmp/launch-fpSStT/org.x:6000: nodename nor servname provided, or not
>>>>>> known
>>>>>> Error displaying error in a popup: couldn't connect to display
>>>>>> "/tmp/launch-fpSStT/org.x:0"
>>>>>>
>>>>>> --aryeh
>>>>>>
>>>>>> On 9/28/10 1:46 PM, Steve Pieper wrote:
>>>>>>> Hmmm -- interesting - it looks like that library file got corrupted
>>>>>>> during the download/extraction process somehow. The file
>>>>>>> lib/InsightToolkit/libITKFEM.3.18.dylib should exist and have a
>>>>>>> size of
>>>>>>> 984296 bytes. Maybe try re-downloading and extracting?
>>>>>>>
>>>>>>> -Steve
>>>>>>>
>>>>>>> On 09/27/2010 11:36 PM, Aryeh Weiss wrote:
>>>>>>>>
>>>>>>>> Thank you for your reply. Here is the error message when I run from
>>>>>>>> the
>>>>>>>> top of the tree:
>>>>>>>> aryeh-weisss-macbookpro52-2:Slicer3-3.6.1-2010-08-20-darwin-x86
>>>>>>>> amw$
>>>>>>>> ./Slicer3
>>>>>>>> Setting up launch environment...
>>>>>>>> dyld: Library not loaded:
>>>>>>>> /Users/hayes/Slicer-3-6/Slicer3-lib/Insight-build/bin/libITKFEM.3.18.dylib
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Referenced from:
>>>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Reason: no suitable image found. Did find:
>>>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/lib/InsightToolkit/libITKFEM.3.18.dylib:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> unknown file type, first eight bytes: 0x00 0x00 0x00 0x00 0xA4 0x87
>>>>>>>> 0xFF
>>>>>>>> 0xBF
>>>>>>>>
>>>>>>>> Launch
>>>>>>>> /Users/amw/Desktop/Slicer3-3.6.1-2010-08-20-darwin-x86/bin/Slicer3-real
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> returned with error: child killed: trace trap
>>>>>>>>
>>>>>>>> CHILDKILLED 16672 SIGTRAP {trace trap}
>>>>>>>> _X11TransSocketINETConnect() can't get address for
>>>>>>>> /tmp/launch-fpSStT/org.x:6000: nodename nor servname provided, or
>>>>>>>> not
>>>>>>>> known
>>>>>>>> Error displaying error in a popup: couldn't connect to display
>>>>>>>> "/tmp/launch-fpSStT/org.x:0"
>>>>>>>>
>>>>>>>> --aryeh
>>>>>>>>
>>>>>>>> On 9/27/10 11:17 PM, Steve Pieper wrote:
>>>>>>>>> p.s. the 3.6.1 binary from 2010-08-20 does work on my intel mac
>>>>>>>>> running
>>>>>>>>> 10.5.8...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 09/27/2010 04:52 PM, Steve Pieper wrote:
>>>>>>>>>> Hi Aryeh -
>>>>>>>>>>
>>>>>>>>>> You shouldn't need to set any variables if you run the Slicer3
>>>>>>>>>> executable at the top level of the extracted archive. What error
>>>>>>>>>> message do you get?
>>>>>>>>>>
>>>>>>>>>> -Steve
>>>>>>>>>>
>>>>>>>>>> On 09/27/2010 03:12 PM, Aryeh Weiss wrote:
>>>>>>>>>>> I just downloaded Slicer3, but it cannot start because it cannot
>>>>>>>>>>> find
>>>>>>>>>>> the dylibs.
>>>>>>>>>>>
>>>>>>>>>>> I found this problem mentioned in earlier posts, but I cannot
>>>>>>>>>>> solve it
>>>>>>>>>>> from those posts.
>>>>>>>>>>> One previous post mentions a setup shell script SlicerSetup.sh
>>>>>>>>>>> (or
>>>>>>>>>>> similar), but this does not exist anywhere in my
>>>>>>>>>>> Slicer3-3.6.1-2010-08-20-darwin-x86 directory tree.
>>>>>>>>>>> I tried setting DYLD_LIBRARY_PATH, but I cannot seem to get it
>>>>>>>>>>> right --
>>>>>>>>>>> something always eventually fails.
>>>>>>>>>>>
>>>>>>>>>>> Any ideas on this would be most appreciated -- it looks like a
>>>>>>>>>>> nice
>>>>>>>>>>> package, but so far I cannot even launch it.
>>>>>>>>>>>
>>>>>>>>>>> --aryeh
>>>>>>>>>> _______________________________________________
>>>>>>>>>> slicer-users mailing list
>>>>>>>>>> slicer-users at bwh.harvard.edu
>>>>>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>>>>>>>>> To unsubscribe: send email to
>>>>>>>>>> slicer-users-request at massmail.spl.harvard.edu with unsubscribe as
>>>>>>>>>> the
>>>>>>>>>> subject
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>


-- 
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051




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