bundler: failed to load command: rspec (/usr/local/bin/rspec)

[Sylfrena]

I'm using Ubuntu 18.04.1 LTS. I was following instructions mentioned at here.

Here is what I did:

$ cd daru

$ sudo apt-get update -qq
$ sudo apt-get install -y libgsl0-dev r-base r-base-dev
$ sudo Rscript -e "install.packages(c('Rserve','irr'),,'http://cran.us.r-project.org')"

$ sudo apt-get install libmagickwand-dev imagemagick

Then install remaining dependencies:
$ bundle install

And run the test suite (should be all green with pending tests):
$ bundle exec rspec

......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/nmatrix-0.2.4/lib/nmatrix/monkeys.rb:49: warning: constant ::Fixnum is deprecated
.........................................................................................................................................................F......................................**................................................................................./home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rserve-client-0.3.5/lib/rserve/rexp/wrapper.rb:26: warning: constant ::Fixnum is deprecated
/home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rserve-client-0.3.5/lib/rserve/rexp/wrapper.rb:56: warning: constant ::Fixnum is deprecated
./home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rserve-client-0.3.5/lib/rserve/rexp/wrapper.rb:26: warning: constant ::Fixnum is deprecated
/home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/rserve-client-0.3.5/lib/rserve/rexp/wrapper.rb:56: warning: constant ::Fixnum is deprecated
...NOTE: Daru::Vector#only_valid is deprecated; use reject_values instead. It will be removed on or after 2016-10-01.
Daru::Vector#only_valid called from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/2.5.0/delegate.rb:83.
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................*................................................................................................................................

bundler: failed to load command: rspec (/home/sumera/.rbenv/versions/2.5.1/bin/rspec)
...: command not found
--- ERROR REPORT TEMPLATE -------------------------------------------------------

Error Report

Questions

Please fill out answers to these questions, it'll help us figure out
why things are going wrong.

• What did you do?

  I ran the command bundle exec rspec

• What did you expect to happen?

  I expected Bundler to run the test suite.

• What happened instead?

Instead, what happened was error occurred saying, bundler: failed to load command: rspec (/usr/local/bin/rspec)

• Have you tried any solutions posted on similar issues in our issue tracker, stack overflow, or google?

I tried google , came across this

• Have you read our issues document, https://github.com/bundler/bundler/blob/master/doc/contributing/ISSUES.md?

yes

Backtrace

Errno::ESPIPE: Illegal seek @ rb_io_tell - <STDERR>
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:86:in `pos'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:86:in `pack_and_write'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:62:in `write_with_packing'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli/exec.rb:81:in `abort'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli/exec.rb:81:in `rescue in kernel_load'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli/exec.rb:65:in `kernel_load'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli/exec.rb:28:in `run'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli.rb:463:in `exec'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/vendor/thor/lib/thor/invocation.rb:126:in `invoke_command'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/vendor/thor/lib/thor.rb:387:in `dispatch'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli.rb:27:in `dispatch'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/vendor/thor/lib/thor/base.rb:466:in `start'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/cli.rb:18:in `start'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/exe/bundle:30:in `block in <top (required)>'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/lib/bundler/friendly_errors.rb:124:in `with_friendly_errors'
  /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/exe/bundle:22:in `<top (required)>'
  /home/sumera/.rbenv/versions/2.5.1/bin/bundle:23:in `load'
  /home/sumera/.rbenv/versions/2.5.1/bin/bundle:23:in `<main>'

Environment

Bundler       2.0.1
  Platforms   ruby, x86_64-linux
Ruby          2.5.1p57 (2018-03-29 revision 63029) [x86_64-linux]
  Full Path   /home/sumera/.rbenv/versions/2.5.1/bin/ruby
  Config Dir  /home/sumera/.rbenv/versions/2.5.1/etc
RubyGems      2.7.6
  Gem Home    /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0
  Gem Path    /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0:/home/sumera/.gem/ruby/2.5.0
  User Path   /home/sumera/.gem/ruby/2.5.0
  Bin Dir     /home/sumera/.rbenv/versions/2.5.1/bin
OpenSSL       
  Compiled    OpenSSL 1.1.0g  2 Nov 2017
  Loaded      OpenSSL 1.1.0g  2 Nov 2017
  Cert File   /usr/lib/ssl/cert.pem
  Cert Dir    /usr/lib/ssl/certs
Tools         
  Git         2.17.1
  RVM         1.29.7 (manual)
  rbenv       rbenv 1.1.1-40-g483e7f9
  chruby      0.3.9

Bundler Build Metadata

Built At          2019-01-04
Git SHA           d7ad2192f
Released Version  true

Bundler settings

bin_path
  Set via BUNDLE_BIN_PATH: "/home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bundler-2.0.1/exe/bundle"
gemfile
  Set via BUNDLE_GEMFILE: "/home/sumera/Elan/daru/Gemfile"

Gemfile

Gemfile

source 'https://rubygems.org'
gemspec

Gemfile.lock

PATH
  remote: .
  specs:
    daru (0.2.1)
      backports
      packable (~> 1.3.9)

GEM
  remote: https://rubygems.org/
  specs:
    activemodel (4.2.11.1)
      activesupport (= 4.2.11.1)
      builder (~> 3.1)
    activerecord (4.2.11.1)
      activemodel (= 4.2.11.1)
      activesupport (= 4.2.11.1)
      arel (~> 6.0)
    activesupport (4.2.11.1)
      i18n (~> 0.7)
      minitest (~> 5.1)
      thread_safe (~> 0.3, >= 0.3.4)
      tzinfo (~> 1.1)
    addressable (2.6.0)
      public_suffix (>= 2.0.2, < 4.0)
    arel (6.0.4)
    ast (2.4.0)
    awesome_print (1.8.0)
    backports (3.12.0)
    builder (3.2.3)
    byebug (11.0.1)
    coderay (1.1.2)
    concurrent-ruby (1.1.5)
    connection_pool (2.2.2)
    crack (0.4.3)
      safe_yaml (~> 1.0.0)
    dbd-sqlite3 (1.2.5)
      dbi (>= 0.4.0)
      sqlite3-ruby
    dbi (0.4.5)
      deprecated (= 2.0.1)
    deprecated (2.0.1)
    diff-lcs (1.3)
    distribution (0.7.3)
    docile (1.3.1)
    domain_name (0.5.20180417)
      unf (>= 0.0.5, < 1.0.0)
    ffi (1.10.0)
    formatador (0.2.5)
    gruff (0.7.0)
      rmagick (~> 2.13, >= 2.13.4)
    gsl (2.1.0.3)
    guard (2.15.0)
      formatador (>= 0.2.4)
      listen (>= 2.7, < 4.0)
      lumberjack (>= 1.0.12, < 2.0)
      nenv (~> 0.1)
      notiffany (~> 0.0)
      pry (>= 0.9.12)
      shellany (~> 0.0)
      thor (>= 0.18.1)
    guard-compat (1.2.1)
    guard-rspec (4.7.3)
      guard (~> 2.1)
      guard-compat (~> 1.1)
      rspec (>= 2.99.0, < 4.0)
    hashdiff (0.3.8)
    http-cookie (1.0.3)
      domain_name (~> 0.5)
    i18n (0.9.5)
      concurrent-ruby (~> 1.0)
    json (2.2.0)
    listen (3.1.5)
      rb-fsevent (~> 0.9, >= 0.9.4)
      rb-inotify (~> 0.9, >= 0.9.7)
      ruby_dep (~> 1.2)
    lumberjack (1.0.13)
    mechanize (2.7.6)
      domain_name (~> 0.5, >= 0.5.1)
      http-cookie (~> 1.0)
      mime-types (>= 1.17.2)
      net-http-digest_auth (~> 1.1, >= 1.1.1)
      net-http-persistent (>= 2.5.2)
      nokogiri (~> 1.6)
      ntlm-http (~> 0.1, >= 0.1.1)
      webrobots (>= 0.0.9, < 0.2)
    method_source (0.9.2)
    mime-types (3.2.2)
      mime-types-data (~> 3.2015)
    mime-types-data (3.2018.0812)
    mini_portile2 (2.4.0)
    minitest (5.11.3)
    nenv (0.3.0)
    net-http-digest_auth (1.4.1)
    net-http-persistent (3.0.0)
      connection_pool (~> 2.2)
    nmatrix (0.2.4)
      packable (~> 1.3, >= 1.3.5)
    nokogiri (1.10.1)
      mini_portile2 (~> 2.4.0)
    notiffany (0.1.1)
      nenv (~> 0.1)
      shellany (~> 0.0)
    ntlm-http (0.1.1)
    nyaplot (0.1.6)
    packable (1.3.10)
      backports
    parallel (1.14.0)
    parser (2.6.2.0)
      ast (~> 2.4.0)
    powerpack (0.1.2)
    pry (0.12.2)
      coderay (~> 1.1.0)
      method_source (~> 0.9.0)
    pry-byebug (3.7.0)
      byebug (~> 11.0)
      pry (~> 0.10)
    public_suffix (3.0.3)
    rainbow (2.2.2)
      rake
    rake (10.5.0)
    rb-fsevent (0.10.3)
    rb-inotify (0.10.0)
      ffi (~> 1.0)
    rmagick (2.16.0)
    rserve-client (0.3.5)
    rspec (3.8.0)
      rspec-core (~> 3.8.0)
      rspec-expectations (~> 3.8.0)
      rspec-mocks (~> 3.8.0)
    rspec-core (3.8.0)
      rspec-support (~> 3.8.0)
    rspec-expectations (3.8.2)
      diff-lcs (>= 1.2.0, < 2.0)
      rspec-support (~> 3.8.0)
    rspec-its (1.2.0)
      rspec-core (>= 3.0.0)
      rspec-expectations (>= 3.0.0)
    rspec-mocks (3.8.0)
      diff-lcs (>= 1.2.0, < 2.0)
      rspec-support (~> 3.8.0)
    rspec-support (3.8.0)
    rubocop (0.49.1)
      parallel (~> 1.10)
      parser (>= 2.3.3.1, < 3.0)
      powerpack (~> 0.1)
      rainbow (>= 1.99.1, < 3.0)
      ruby-progressbar (~> 1.7)
      unicode-display_width (~> 1.0, >= 1.0.1)
    ruby-ole (1.2.12.2)
    ruby-prof (0.17.0)
    ruby-progressbar (1.10.0)
    ruby_dep (1.5.0)
    safe_yaml (1.0.5)
    shellany (0.0.1)
    simplecov (0.16.1)
      docile (~> 1.1)
      json (>= 1.8, < 3)
      simplecov-html (~> 0.10.0)
    simplecov-html (0.10.2)
    spreadsheet (1.1.9)
      ruby-ole (>= 1.0)
    sqlite3 (1.3.13)
    sqlite3-ruby (1.3.3)
      sqlite3 (>= 1.3.3)
    thor (0.20.3)
    thread_safe (0.3.6)
    tzinfo (1.2.5)
      thread_safe (~> 0.1)
    unf (0.1.4)
      unf_ext
    unf_ext (0.0.7.5)
    unicode-display_width (1.5.0)
    webmock (3.5.1)
      addressable (>= 2.3.6)
      crack (>= 0.3.2)
      hashdiff
    webrobots (0.1.2)

PLATFORMS
  ruby

DEPENDENCIES
  activerecord (~> 4.0)
  awesome_print
  bundler (>= 1.10)
  daru!
  dbd-sqlite3
  dbi
  distribution (~> 0.7)
  gruff
  gsl (~> 2.1.0.2)
  guard-rspec
  mechanize
  nmatrix (~> 0.2.1)
  nokogiri
  nyaplot (~> 0.1.5)
  pry (~> 0.10)
  pry-byebug
  rake (~> 10.5)
  rserve-client (~> 0.3)
  rspec (~> 3.4)
  rspec-its
  rubocop (~> 0.49.0)
  ruby-prof
  simplecov
  spreadsheet (~> 1.1.1)
  sqlite3 (~> 1.3.13)
  webmock

BUNDLED WITH
   2.0.1

Gemspecs

daru.gemspec

# coding: utf-8
$:.unshift File.expand_path("../lib", __FILE__)

require 'daru/version.rb'

Daru::DESCRIPTION = <<MSG
Daru (Data Analysis in RUby) is a library for analysis, manipulation and visualization
of data. Daru works seamlessly accross interpreters and leverages interpreter-specific
optimizations whenever they are available.

It is the default data storage gem for all the statsample gems (glm, timeseries, etc.)
and can be used with many others like mixed_models, gnuplotrb, nyaplot and iruby.
MSG

Gem::Specification.new do |spec|
  spec.name          = 'daru'
  spec.version       = Daru::VERSION
  spec.authors       = ['Sameer Deshmukh']
  spec.email         = ['[email protected]']
  spec.summary       = %q{Data Analysis in RUby}
  spec.description   = Daru::DESCRIPTION
  spec.homepage      = "https://github.com/v0dro/daru"
  spec.license       = 'BSD-2'

  spec.files         = `git ls-files -z`.split("\x0")
  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
  spec.require_paths = ["lib"]

  spec.add_runtime_dependency 'backports'

  # it is required by NMatrix, yet we want to specify clearly which minimal version is OK
  spec.add_runtime_dependency 'packable', '~> 1.3.9'

  spec.add_development_dependency 'spreadsheet', '~> 1.1.1'
  spec.add_development_dependency 'bundler', '>= 1.10'
  spec.add_development_dependency 'rake', '~>10.5'
  spec.add_development_dependency 'pry', '~> 0.10'
  spec.add_development_dependency 'pry-byebug'
  spec.add_development_dependency 'rserve-client', '~> 0.3'
  spec.add_development_dependency 'rspec', '~> 3.4'
  spec.add_development_dependency 'rspec-its'
  spec.add_development_dependency 'awesome_print'
  spec.add_development_dependency 'nyaplot', '~> 0.1.5'
  spec.add_development_dependency 'nmatrix', '~> 0.2.1'
  spec.add_development_dependency 'distribution', '~> 0.7'
  spec.add_development_dependency 'gsl', '~>2.1.0.2'
  spec.add_development_dependency 'dbd-sqlite3'
  spec.add_development_dependency 'dbi'
  spec.add_development_dependency 'activerecord', '~> 4.0'
  spec.add_development_dependency 'mechanize'
  # issue : https://github.com/SciRuby/daru/issues/493 occured 
  # with latest version of sqlite3
  spec.add_development_dependency  'sqlite3', '~> 1.3.13'
  spec.add_development_dependency 'rubocop', '~> 0.49.0'
  spec.add_development_dependency 'ruby-prof'
  spec.add_development_dependency 'simplecov'
  spec.add_development_dependency 'gruff'
  spec.add_development_dependency 'webmock'

  if RUBY_VERSION < '2.1.0'
    spec.add_development_dependency 'nokogiri', '<= 1.6.8.1'
  else
    spec.add_development_dependency 'nokogiri'
  end
  if RUBY_VERSION >= '2.2.5'
    spec.add_development_dependency 'guard-rspec'
  end
end

--- TEMPLATE END ----------------------------------------------------------------

Unfortunately, an unexpected error occurred, and Bundler cannot continue.

First, try this link to see if there are any existing issue reports for this error:
https://github.com/bundler/bundler/search?q=Illegal+seek+%40+rb_io_tell+-+%3CSTDERR%3E&type=Issues

If there aren't any reports for this error yet, please create copy and paste the report template above into a new issue. Don't forget to anonymize any private data! The new issue form is located at:
https://github.com/bundler/bundler/issues/new
Traceback (most recent call last):
9: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-0.16.1/lib/simplecov/defaults.rb:27:in block in <top (required)>' 8: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-0.16.1/lib/simplecov.rb:200:in run_exit_tasks!'
7: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-0.16.1/lib/simplecov/configuration.rb:182:in block in at_exit' 6: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-0.16.1/lib/simplecov/result.rb:48:in format!'
5: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-html-0.10.2/lib/simplecov-html.rb:25:in format' 4: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-html-0.10.2/lib/simplecov-html.rb:25:in puts'
3: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/simplecov-html-0.10.2/lib/simplecov-html.rb:25:in puts' 2: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:62:in write_with_packing'
1: from /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:86:in pack_and_write' /home/sumera/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/packable-1.3.10/lib/packable/extensions/io.rb:86:in pos': Illegal seek @ rb_io_tell - (Errno::ESPIPE)

[Shekharrajak]

I didn't understand why you are getting this, in between :

bundler: failed to load command: rspec (/home/sumera/.rbenv/versions/2.5.1/bin/rspec)
...: command not found

[Sylfrena]

@Shekharrajak Yes, it is very puzzling. Initially I thought the command is just unable to access rspec but even after I changed and verified paths, still no show.

[Shekharrajak]

Can you please try with different Ruby version - like Ruby 2.4 ?

[Shekharrajak]

Related issue https://github.com/SciRuby/packable/issues/4

[Shekharrajak]

Travis is configured only for Ruby < 2.5, so please use lower Ruby version for now or need to work in it to make this rspec compatible for higher ruby version.

[Sylfrena]

@Shekharrajak
Thanks so much! Changing the Ruby version worked like a charm!
I think it would be helpful for newbie contributors if in CONTRIBUTING.md , this issue was mentioned. May I make a pull request for the same?
I'll close this issue for now.

[Shekharrajak]

Yes, that will be helpful. You can also add link of this issue, so that anyone can explore it further.

[Sylfrena]

@Shekharrajak
I made a PR regarding this here. Please let me know if there are any changes I need to make.

[Shekharrajak]

Actual error is :

/gems/packable-1.3.10/lib/packable/extensions/io.rb:86:in `pos': Illegal seek @ rb_io_tell - <STDOUT> (Errno::ESPIPE)