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November 9, 2016 18:33
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Bel.rb Installation trouble
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[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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