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@cthoyt
Created November 9, 2016 18:33
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Bel.rb Installation trouble
[544] [19:04] [cthoyt@microvac:~]
$ rvm use 2.3.0 --install
ruby-2.3.0 is not installed - installing.
Searching for binary rubies, this might take some time.
No binary rubies available for: osx/10.12/x86_64/ruby-2.3.0.
Continuing with compilation. Please read 'rvm help mount' to get more information on binary rubies.
Checking requirements for osx.
Certificates in '/usr/local/etc/openssl/cert.pem' are already up to date.
Requirements installation successful.
Installing Ruby from source to: /Users/cthoyt/.rvm/rubies/ruby-2.3.0, this may take a while depending on your cpu(s)...
ruby-2.3.0 - #downloading ruby-2.3.0, this may take a while depending on your connection...
ruby-2.3.0 - #extracting ruby-2.3.0 to /Users/cthoyt/.rvm/src/ruby-2.3.0....
ruby-2.3.0 - #configuring...........................................................
ruby-2.3.0 - #post-configuration.
ruby-2.3.0 - #compiling..............................................................
ruby-2.3.0 - #installing.........
ruby-2.3.0 - #making binaries executable..
Installed rubygems 2.5.1 is newer than 2.4.8 provided with installed ruby, skipping installation, use --force to force installation.
ruby-2.3.0 - #gemset created /Users/cthoyt/.rvm/gems/ruby-2.3.0@global
ruby-2.3.0 - #importing gemset /Users/cthoyt/.rvm/gemsets/global.gems...............................................
ruby-2.3.0 - #generating global wrappers........
ruby-2.3.0 - #gemset created /Users/cthoyt/.rvm/gems/ruby-2.3.0
ruby-2.3.0 - #importing gemsetfile /Users/cthoyt/.rvm/gemsets/default.gems evaluated to empty gem list
ruby-2.3.0 - #generating default wrappers........
ruby-2.3.0 - #adjusting #shebangs for (gem irb erb ri rdoc testrb rake).
Install of ruby-2.3.0 - #complete
Ruby was built without documentation, to build it run: rvm docs generate-ri
Using /Users/cthoyt/.rvm/gems/ruby-2.3.0
[545] [19:10] [cthoyt@microvac:~]
$ which gem
/Users/cthoyt/.rvm/rubies/ruby-2.3.0/bin/gem
[546] [19:12] [cthoyt@microvac:~]
$ gem --version
2.5.1
[547] [19:12] [cthoyt@microvac:~]
$ ruby --version
ruby 2.3.0p0 (2015-12-25 revision 53290) [x86_64-darwin16]
[548] [19:12] [cthoyt@microvac:~]
$ which ruby
/Users/cthoyt/.rvm/rubies/ruby-2.3.0/bin/ruby
[549] [19:12] [cthoyt@microvac:~]
$ gem install bel
Fetching: ffi-1.9.8.gem (100%)
Building native extensions. This could take a while...
Successfully installed ffi-1.9.8
Building native extensions. This could take a while...
Successfully installed bel-0.7.0
2 gems installed
[552] [19:26] [cthoyt@microvac:~]
$ gem install rdf addressable uuid rdf-turtle
Fetching: link_header-0.0.8.gem (100%)
Successfully installed link_header-0.0.8
Fetching: concurrent-ruby-1.0.2.gem (100%)
Successfully installed concurrent-ruby-1.0.2
Fetching: hamster-3.0.0.gem (100%)
Successfully installed hamster-3.0.0
Fetching: rdf-2.1.0.gem (100%)
Successfully installed rdf-2.1.0
Fetching: public_suffix-2.0.4.gem (100%)
Successfully installed public_suffix-2.0.4
Fetching: addressable-2.5.0.gem (100%)
Successfully installed addressable-2.5.0
Fetching: systemu-2.6.5.gem (100%)
Successfully installed systemu-2.6.5
Fetching: macaddr-1.7.1.gem (100%)
Successfully installed macaddr-1.7.1
Fetching: uuid-2.3.8.gem (100%)
Successfully installed uuid-2.3.8
Fetching: sxp-1.0.0.gem (100%)
Successfully installed sxp-1.0.0
Fetching: ebnf-1.0.1.gem (100%)
Successfully installed ebnf-1.0.1
Fetching: rdf-turtle-2.0.0.gem (100%)
Successfully installed rdf-turtle-2.0.0
12 gems installed
[553] [19:26] [cthoyt@microvac:~]
$ bel --help
Usage: bel [OPTIONS]... COMMAND
A set of commands to process BEL knowledge.
Subcommands:
bel2rdf
compare
parse
rdfschema
summarize
translate
upgrade
plugins
generate
remapfile
bel 0.7.0
Copyright (C) 2016 OpenBEL
Apache License, Version 2.0, January 2004
http://www.apache.org/licenses/
Options:
-v, --verbose Verbose output.
-e, --version Print version and exit
-h, --help Show this message
[555] [19:27] [cthoyt@microvac:~]
$ bel upgrade --help
Usage: bel [OPTIONS]... upgrade [OPTIONS]
Upgrades BEL knowledge and annotation.
Options:
-b, --bel=<s> The BEL script to parse and output. If not provided the default is to read from standard in (STDIN).
-c, --changelog=<s> The changelog JSON file or URL. (Default: http://resource.belframework.org/belframework/latest-release/change_log.json)
-h, --help Show this message
[556] [19:27] [cthoyt@microvac:~]
$ bel bel2rdf --help
Usage: bel [OPTIONS]... bel2rdf [OPTIONS]
Converts BEL to RDF.
Options:
-b, --bel=<s> The BEL script to parse and output (Defaults to STDIN).
-f, --format=<s> The RDF format to output. (Default: ntriples)
-s, --schema Includes the BEL RDFS schema in RDF output.
-p, --rdf-prefix-file=<s> A YAML file mapping prefix containing key/value pairs. The key is an RDF prefix to use in the RDF output; the value is the RDF URI for that prefix. For example, belv:
'http://www.openbel.org/vocabulary/'
-r, --remap-file=<s> A YAML file that remaps annotation and namespace definitions. Run "bel remapfile" to get an example of the YAML format.
-h, --help Show this message
[557] [19:27] [cthoyt@microvac:~]
$ bel bel2rdf -b ~/Desktop/small_corpus.bel > ~/Desktop/small_corpus.rdf
/Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/rdf-2.1.0/lib/rdf.rb:66:in `const_missing': uninitialized constant RDF::SKOS (NameError)
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/rdf/bel_schema.rb:197:in `<module:BELRDF>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/rdf/bel_schema.rb:2:in `<top (required)>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/rdf/translator.rb:6:in `require_relative'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/rdf/translator.rb:6:in `<top (required)>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/ntriples.rb:14:in `require_relative'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translator/plugins/ntriples.rb:14:in `create_translator'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/lib/bel/translate.rb:73:in `translator'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/bin/bel2rdf.rb:84:in `validate_translator!'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/bin/bel2rdf.rb:106:in `<top (required)>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/bin/bel:103:in `require_relative'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/bin/bel:103:in `run'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/gems/bel-0.7.0/bin/bel:583:in `<top (required)>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/bin/bel:23:in `load'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/bin/bel:23:in `<main>'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/bin/ruby_executable_hooks:15:in `eval'
from /Users/cthoyt/.rvm/gems/ruby-2.3.0/bin/ruby_executable_hooks:15:in `<main>'
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