Re: [Gmod-ajax] [apollo] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

[Nathan D. <nat...@lb...>]

That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


> On Jul 29, 2018, at 7:39 PM, Robert Buels <rb...@gm...> wrote:
> 
> Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?
> 
> 
> On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Unfortunately Perl + Mac has become more problematic.  
> 
> I’m assuming you’re using home-brew perl? 
> 
> I’ll look at some better solutions this week and reply here.  
> 
> Some workarounds:
> 
> 1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.
> 
> 2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  
> 
> 3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  
> 
> Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 
> 
> Nathan
> 
> 
>> On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <you...@va... <mailto:you...@va...>> wrote:
>> 
>> Hi
>> 
>> I can run Apollo, but got error when I wanna to add annotations:
>> 
>> Here is the error info:
>> 
>> Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl <http://add_features_from_gff3_to_annotations.pl/> -h
>> 
>> Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
>> dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
>>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>>   Expected in: flat namespace
>> 
>> dyld: Symbol not found: _Perl_xs_handshake
>>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>>   Expected in: flat namespace
>> 
>> Abort trap: 6
>> 
>> Best
>> Youhuang Bai
>> 
>> 
>> 
>> 
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