Re: [Gmod-ajax] Jbrowse error

[Colin <col...@gm...>]

A previous thread suggests simply force installing this dependency

http://gmod.827538.n3.nabble.com/Gmod-ajax-JBrowse-Dependencies-Unable-to-install-Heap-Simple-Perl-and-Heap-Simple-XS-td4053362.html

-Colin

On Thu, Jun 27, 2019 at 2:12 PM Beppu, Lan W <lb...@fr...> wrote:

> Hi Colin,
>
>
>
> I’m getting this error below. Do you have any suggestions to what I should
> try?
>
>
>
> Thanks,
>
> Lan
>
>
>
> Can't locate Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0.13) in @INC.
> This probably means you didn't install any of them. (@INC contains:
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5
> /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
> /Network/Library/Perl/5.18/darwin-thread-multi-2level
> /Network/Library/Perl/5.18
> /Library/Perl/Updates/5.18.4/darwin-thread-multi-2level
> /Library/Perl/Updates/5.18.4
> /System/Library/Perl/5.18/darwin-thread-multi-2level
> /System/Library/Perl/5.18
> /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.18 .) at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> Compilation failed in require at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> Compilation failed in require at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
> line 8.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
> line 8.
>
> Compilation failed in require at (eval 7) line 2.
>
>        ...propagated at /System/Library/Perl/5.18/base.pm line 84.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
>        require Bio/JBrowse/Cmd/BioDBToJson.pm called at bin/
> biodb-to-json.pl line 7
>
>        main::BEGIN() called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
>        eval {...} called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
> Compilation failed in require at bin/biodb-to-json.pl line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at bin/
> biodb-to-json.pl line 7
>
>        main::BEGIN() called at bin/biodb-to-json.pl line 7
>
>        eval {...} called at bin/biodb-to-json.pl line 7
>
> BEGIN failed--compilation aborted at bin/biodb-to-json.pl line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at bin/
> biodb-to-json.pl line 7
>
>
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Tuesday, June 25, 2019 at 1:53 PM
> *To: *"Beppu, Lan W" <lb...@fr...>, gmod-ajax <
> gmo...@li...>
> *Subject: *Re: [Gmod-ajax] Jbrowse error
>
>
>
> Hi there,
>
>
>
> The JBrowse root directory is the same directory that the setup.sh file is
> in, so you can simply "cd" into this directory and then run ./setup.sh
>
>
>
> -Colin
>
>
>
> On Tue, Jun 25, 2019 at 4:29 PM Beppu, Lan W <lb...@fr...> wrote:
>
> Hello,
>
>
>
> How do I get into the jbrowse root directory? Would that be on my local
> directory?
>
>
>
> Thanks,
>
> Lan
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Friday, June 14, 2019 at 8:59 AM
> *To: *"Spencer, Kaolu L" <ksp...@fr...>
> *Cc: *"gmo...@li..." <gmo...@li...>,
> "Beppu, Lan W" <lb...@fr...>
> *Subject: *Re: [Gmod-ajax] Jbrowse error
>
>
>
> Hi there,
>
>
>
> I think from looking at the setup.log that you didn't run the setup.sh
> while inside the jbrowse root directory
>
>
>
> You have to be inside the jbrowse directory and then run ./setup.sh
>
>
>
> Hope that helps
>
>
>
> -Colin
>
>
>
> On Fri, Jun 14, 2019 at 11:55 AM Spencer, Kaolu L <ksp...@fr...>
> wrote:
>
>
> * Kaolu Spencer*
>
> Service Desk Engineer II
> 206-667-2431
> ksp...@fr...
>
>
>
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