[slicer-users] problem starting with OSX 10.5.8

Steve Pieper pieper at bwh.harvard.edu
Thu Sep 30 17:16:23 EDT 2010


Ahh - excellent clue! - these 0 length files should actually be symbolic 
links.  That is, they should look like this:

common:vtk-5.6 pieper$ ls -l libvtkzl*
-rwxr-xr-x@ 1 pieper  staff  84300 Mar 30  2010 libvtkzlib.5.6.0.dylib
lrwxr-xr-x@ 1 pieper  staff     22 Apr 27 16:10 libvtkzlib.5.6.dylib -> 
libvtkzlib.5.6.0.dylib
lrwxr-xr-x@ 1 pieper  staff     20 Apr 27 16:10 libvtkzlib.dylib -> 
libvtkzlib.5.6.dylib


I wonder if this is because of the disk format of the volume where you 
extracted slicer - is it an external widows-formated drive by any chance?

If you can try on a mac-formatted drive (like the root volume)?

Steve

On 09/30/2010 05:03 PM, Aryeh Weiss wrote:
>
>
> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>



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