カクカクしかじか

技術的なアレコレ

Dockerでコンテナ内にbundle installされない問題の解決法

Docker MongoDB Ruby on Rails mongoid エラー解決

前提

こちらの記事はDockerに対して不慣れな人間が書いているので、そらそうやろ！という内容が含まれます。
それでも個人用メモとして放流します。

技術要素

Rails 5.2.2.1
Ruby 2.5.1
mongodb 4.0.6

Dockerを扱うディレクトリ構成

  • アプリディレクトリ/
    • Gemfile
    • Gemfile.lock
    • Dockerfile
    • docker-compose.yml

遭遇したエラー

docker-compose run web bundle install --path vendor/bundler を実行した後なのに docker-compose up でサーバーを起動しようとすると Run bundle install to install missing gems. というエラーが出てしまう...

Could not find bson-4.4.2 in any of the sources
Run `bundle install` to install missing gems.

bson-4.4.2 が無い？(bundle installしたのになぜ？)

関連しそうなファイルの構成

Gemfile

source 'https://rubygems.org'
git_source(:github) { |repo| "https://github.com/#{repo}.git" }

ruby '2.5.1'

# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 5.2.2', '>= 5.2.2.1'
# Use Puma as the app server
gem 'puma', '~> 3.11'
# Use SCSS for stylesheets
gem 'sass-rails', '~> 5.0'
# Use Uglifier as compressor for JavaScript assets
gem 'uglifier', '>= 1.3.0'
# See https://github.com/rails/execjs#readme for more supported runtimes
# gem 'mini_racer', platforms: :ruby

# Use CoffeeScript for .coffee assets and views
gem 'coffee-rails', '~> 4.2'
# Turbolinks makes navigating your web application faster. Read more: https://github.com/turbolinks/turbolinks
gem 'turbolinks', '~> 5'
# Build JSON APIs with ease. Read more: https://github.com/rails/jbuilder
gem 'jbuilder', '~> 2.5'
# Use Redis adapter to run Action Cable in production
# gem 'redis', '~> 4.0'
# Use ActiveModel has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use Capistrano for deployment
# gem 'capistrano-rails', group: :development

# Reduces boot times through caching; required in config/boot.rb
gem 'bootsnap', '>= 1.1.0', require: false

gem 'mongoid'

group :development, :test do
  # Call 'byebug' anywhere in the code to stop execution and get a debugger console
  gem 'byebug', platforms: [:mri, :mingw, :x64_mingw]
end

group :development do
  # Access an interactive console on exception pages or by calling 'console' anywhere in the code.
  gem 'web-console', '>= 3.3.0'
  gem 'listen', '>= 3.0.5', '< 3.2'
  # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
  gem 'spring'
  gem 'spring-watcher-listen', '~> 2.0.0'
end

group :test do
  # Adds support for Capybara system testing and selenium driver
  gem 'capybara', '>= 2.15'
  gem 'selenium-webdriver'
  # Easy installation and use of chromedriver to run system tests with Chrome
  gem 'chromedriver-helper'
end

# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

Gemfile.lock

GEM
  remote: https://rubygems.org/
  specs:
    actioncable (5.2.2.1)
      actionpack (= 5.2.2.1)
      nio4r (~> 2.0)
      websocket-driver (>= 0.6.1)
    actionmailer (5.2.2.1)
      actionpack (= 5.2.2.1)
      actionview (= 5.2.2.1)
      activejob (= 5.2.2.1)
      mail (~> 2.5, >= 2.5.4)
      rails-dom-testing (~> 2.0)
    actionpack (5.2.2.1)
      actionview (= 5.2.2.1)
      activesupport (= 5.2.2.1)
      rack (~> 2.0)
      rack-test (>= 0.6.3)
      rails-dom-testing (~> 2.0)
      rails-html-sanitizer (~> 1.0, >= 1.0.2)
    actionview (5.2.2.1)
      activesupport (= 5.2.2.1)
      builder (~> 3.1)
      erubi (~> 1.4)
      rails-dom-testing (~> 2.0)
      rails-html-sanitizer (~> 1.0, >= 1.0.3)
    activejob (5.2.2.1)
      activesupport (= 5.2.2.1)
      globalid (>= 0.3.6)
    activemodel (5.2.2.1)
      activesupport (= 5.2.2.1)
    activerecord (5.2.2.1)
      activemodel (= 5.2.2.1)
      activesupport (= 5.2.2.1)
      arel (>= 9.0)
    activestorage (5.2.2.1)
      actionpack (= 5.2.2.1)
      activerecord (= 5.2.2.1)
      marcel (~> 0.3.1)
    activesupport (5.2.2.1)
      concurrent-ruby (~> 1.0, >= 1.0.2)
      i18n (>= 0.7, < 2)
      minitest (~> 5.1)
      tzinfo (~> 1.1)
    addressable (2.6.0)
      public_suffix (>= 2.0.2, < 4.0)
    archive-zip (0.12.0)
      io-like (~> 0.3.0)
    arel (9.0.0)
    bindex (0.5.0)
    bootsnap (1.4.1)
      msgpack (~> 1.0)
    bson (4.4.2)
    builder (3.2.3)
    byebug (11.0.1)
    capybara (3.15.0)
      addressable
      mini_mime (>= 0.1.3)
      nokogiri (~> 1.8)
      rack (>= 1.6.0)
      rack-test (>= 0.6.3)
      regexp_parser (~> 1.2)
      xpath (~> 3.2)
    childprocess (0.9.0)
      ffi (~> 1.0, >= 1.0.11)
    chromedriver-helper (2.1.0)
      archive-zip (~> 0.10)
      nokogiri (~> 1.8)
    coffee-rails (4.2.2)
      coffee-script (>= 2.2.0)
      railties (>= 4.0.0)
    coffee-script (2.4.1)
      coffee-script-source
      execjs
    coffee-script-source (1.12.2)
    concurrent-ruby (1.1.5)
    crass (1.0.4)
    erubi (1.8.0)
    execjs (2.7.0)
    ffi (1.10.0)
    globalid (0.4.2)
      activesupport (>= 4.2.0)
    i18n (1.6.0)
      concurrent-ruby (~> 1.0)
    io-like (0.3.0)
    jbuilder (2.8.0)
      activesupport (>= 4.2.0)
      multi_json (>= 1.2)
    listen (3.1.5)
      rb-fsevent (~> 0.9, >= 0.9.4)
      rb-inotify (~> 0.9, >= 0.9.7)
      ruby_dep (~> 1.2)
    loofah (2.2.3)
      crass (~> 1.0.2)
      nokogiri (>= 1.5.9)
    mail (2.7.1)
      mini_mime (>= 0.1.1)
    marcel (0.3.3)
      mimemagic (~> 0.3.2)
    method_source (0.9.2)
    mimemagic (0.3.3)
    mini_mime (1.0.1)
    mini_portile2 (2.4.0)
    minitest (5.11.3)
    mongo (2.7.1)
      bson (>= 4.4.2, < 5.0.0)
    mongoid (7.0.2)
      activemodel (>= 5.1, < 6.0.0)
      mongo (>= 2.5.1, < 3.0.0)
    msgpack (1.2.9)
    multi_json (1.13.1)
    nio4r (2.3.1)
    nokogiri (1.10.1)
      mini_portile2 (~> 2.4.0)
    public_suffix (3.0.3)
    puma (3.12.1)
    rack (2.0.6)
    rack-test (1.1.0)
      rack (>= 1.0, < 3)
    rails (5.2.2.1)
      actioncable (= 5.2.2.1)
      actionmailer (= 5.2.2.1)
      actionpack (= 5.2.2.1)
      actionview (= 5.2.2.1)
      activejob (= 5.2.2.1)
      activemodel (= 5.2.2.1)
      activerecord (= 5.2.2.1)
      activestorage (= 5.2.2.1)
      activesupport (= 5.2.2.1)
      bundler (>= 1.3.0)
      railties (= 5.2.2.1)
      sprockets-rails (>= 2.0.0)
    rails-dom-testing (2.0.3)
      activesupport (>= 4.2.0)
      nokogiri (>= 1.6)
    rails-html-sanitizer (1.0.4)
      loofah (~> 2.2, >= 2.2.2)
    railties (5.2.2.1)
      actionpack (= 5.2.2.1)
      activesupport (= 5.2.2.1)
      method_source
      rake (>= 0.8.7)
      thor (>= 0.19.0, < 2.0)
    rake (12.3.2)
    rb-fsevent (0.10.3)
    rb-inotify (0.10.0)
      ffi (~> 1.0)
    regexp_parser (1.3.0)
    ruby_dep (1.5.0)
    rubyzip (1.2.2)
    sass (3.7.3)
      sass-listen (~> 4.0.0)
    sass-listen (4.0.0)
      rb-fsevent (~> 0.9, >= 0.9.4)
      rb-inotify (~> 0.9, >= 0.9.7)
    sass-rails (5.0.7)
      railties (>= 4.0.0, < 6)
      sass (~> 3.1)
      sprockets (>= 2.8, < 4.0)
      sprockets-rails (>= 2.0, < 4.0)
      tilt (>= 1.1, < 3)
    selenium-webdriver (3.141.0)
      childprocess (~> 0.5)
      rubyzip (~> 1.2, >= 1.2.2)
    spring (2.0.2)
      activesupport (>= 4.2)
    spring-watcher-listen (2.0.1)
      listen (>= 2.7, < 4.0)
      spring (>= 1.2, < 3.0)
    sprockets (3.7.2)
      concurrent-ruby (~> 1.0)
      rack (> 1, < 3)
    sprockets-rails (3.2.1)
      actionpack (>= 4.0)
      activesupport (>= 4.0)
      sprockets (>= 3.0.0)
    thor (0.20.3)
    thread_safe (0.3.6)
    tilt (2.0.9)
    turbolinks (5.2.0)
      turbolinks-source (~> 5.2)
    turbolinks-source (5.2.0)
    tzinfo (1.2.5)
      thread_safe (~> 0.1)
    uglifier (4.1.20)
      execjs (>= 0.3.0, < 3)
    web-console (3.7.0)
      actionview (>= 5.0)
      activemodel (>= 5.0)
      bindex (>= 0.4.0)
      railties (>= 5.0)
    websocket-driver (0.7.0)
      websocket-extensions (>= 0.1.0)
    websocket-extensions (0.1.3)
    xpath (3.2.0)
      nokogiri (~> 1.8)

PLATFORMS
  ruby

DEPENDENCIES
  bootsnap (>= 1.1.0)
  byebug
  capybara (>= 2.15)
  chromedriver-helper
  coffee-rails (~> 4.2)
  jbuilder (~> 2.5)
  listen (>= 3.0.5, < 3.2)
  mongoid
  puma (~> 3.11)
  rails (~> 5.2.2, >= 5.2.2.1)
  sass-rails (~> 5.0)
  selenium-webdriver
  spring
  spring-watcher-listen (~> 2.0.0)
  turbolinks (~> 5)
  tzinfo-data
  uglifier (>= 1.3.0)
  web-console (>= 3.3.0)

RUBY VERSION
   ruby 2.5.1p57

BUNDLED WITH
   1.17.3

Dockerfile

FROM ruby:2.5.1
RUN apt-get update -qq && apt-get install -y build-essential nodejs
RUN mkdir /app
WORKDIR /app
COPY Gemfile /app/Gemfile
COPY Gemfile.lock /app/Gemfile.lock
RUN gem install bundler
RUN bundle install
COPY . /app

docker-compose.yml

version: '3'
services:
  web:
    build: .
    command: bundle exec rails s -p 3000 -b '0.0.0.0'
    volumes:
      - .:/app
    ports:
      - 3000:3000
    depends_on:
      - db
    tty: true
    stdin_open: true
  db:
    image: mongo:4.0.6
    volumes:
      - ./docker/mongodb/data:/data/db
volumes:
  db-volume:

解決法

キャッシュで bundle install が実行されない場合があるっぽい！
docker-compose build --no-cache を実行する

https://www.udemy.com/rails-kj/learn/v4/questions/6375408

$ docker-compose build --no-cache
db uses an image, skipping
Building web
Step 1/9 : FROM ruby:2.5.1
 ---> 3c8181e703d2
Step 2/9 : RUN apt-get update -qq && apt-get install -y build-essential nodejs
 ---> Running in e9fe91dea4b5
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  dpkg-dev fakeroot libalgorithm-diff-perl libalgorithm-diff-xs-perl
  libalgorithm-merge-perl libfakeroot libuv1
Suggested packages:
  debian-keyring
The following NEW packages will be installed:
  build-essential dpkg-dev fakeroot libalgorithm-diff-perl
  libalgorithm-diff-xs-perl libalgorithm-merge-perl libfakeroot libuv1 nodejs
0 upgraded, 9 newly installed, 0 to remove and 49 not upgraded.
Need to get 5331 kB of archives.
After this operation, 17.0 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian stretch/main amd64 dpkg-dev all 1.18.25 [1595 kB]
Get:2 http://deb.debian.org/debian stretch/main amd64 build-essential amd64 12.3 [7346 B]
Get:3 http://deb.debian.org/debian stretch/main amd64 libfakeroot amd64 1.21-3.1 [45.7 kB]
Get:4 http://deb.debian.org/debian stretch/main amd64 fakeroot amd64 1.21-3.1 [85.6 kB]
Get:5 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-perl all 1.19.03-1 [48.7 kB]
Get:6 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-xs-perl amd64 0.04-4+b2 [11.6 kB]
Get:7 http://deb.debian.org/debian stretch/main amd64 libalgorithm-merge-perl all 0.08-3 [12.7 kB]
Get:8 http://deb.debian.org/debian stretch/main amd64 libuv1 amd64 1.9.1-3 [84.4 kB]
Get:9 http://deb.debian.org/debian stretch/main amd64 nodejs amd64 4.8.2~dfsg-1 [3440 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 5331 kB in 3s (1774 kB/s)
Selecting previously unselected package dpkg-dev.
(Reading database ... 29376 files and directories currently installed.)
Preparing to unpack .../0-dpkg-dev_1.18.25_all.deb ...
Unpacking dpkg-dev (1.18.25) ...
Selecting previously unselected package build-essential.
Preparing to unpack .../1-build-essential_12.3_amd64.deb ...
Unpacking build-essential (12.3) ...
Selecting previously unselected package libfakeroot:amd64.
Preparing to unpack .../2-libfakeroot_1.21-3.1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.21-3.1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../3-fakeroot_1.21-3.1_amd64.deb ...
Unpacking fakeroot (1.21-3.1) ...
Selecting previously unselected package libalgorithm-diff-perl.
Preparing to unpack .../4-libalgorithm-diff-perl_1.19.03-1_all.deb ...
Unpacking libalgorithm-diff-perl (1.19.03-1) ...
Selecting previously unselected package libalgorithm-diff-xs-perl.
Preparing to unpack .../5-libalgorithm-diff-xs-perl_0.04-4+b2_amd64.deb ...
Unpacking libalgorithm-diff-xs-perl (0.04-4+b2) ...
Selecting previously unselected package libalgorithm-merge-perl.
Preparing to unpack .../6-libalgorithm-merge-perl_0.08-3_all.deb ...
Unpacking libalgorithm-merge-perl (0.08-3) ...
Selecting previously unselected package libuv1:amd64.
Preparing to unpack .../7-libuv1_1.9.1-3_amd64.deb ...
Unpacking libuv1:amd64 (1.9.1-3) ...
Selecting previously unselected package nodejs.
Preparing to unpack .../8-nodejs_4.8.2~dfsg-1_amd64.deb ...
Unpacking nodejs (4.8.2~dfsg-1) ...
Setting up libuv1:amd64 (1.9.1-3) ...
Setting up dpkg-dev (1.18.25) ...
Processing triggers for libc-bin (2.24-11+deb9u3) ...
Setting up libfakeroot:amd64 (1.21-3.1) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up nodejs (4.8.2~dfsg-1) ...
update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode
Setting up build-essential (12.3) ...
Setting up fakeroot (1.21-3.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libalgorithm-merge-perl (0.08-3) ...
Setting up libalgorithm-diff-xs-perl (0.04-4+b2) ...
Processing triggers for libc-bin (2.24-11+deb9u3) ...
Removing intermediate container e9fe91dea4b5
 ---> c3b444433c3f
Step 3/9 : RUN mkdir /app
 ---> Running in d9a2a7303e84
Removing intermediate container d9a2a7303e84
 ---> 56a13202e842
Step 4/9 : WORKDIR /app
 ---> Running in bbd450d4f4b4
Removing intermediate container bbd450d4f4b4
 ---> 533f815a4d7f
Step 5/9 : COPY Gemfile /app/Gemfile
 ---> 794f51b7f83d
Step 6/9 : COPY Gemfile.lock /app/Gemfile.lock
 ---> b718ae62f2c7
Step 7/9 : RUN gem install bundler
 ---> Running in 3ea22bf774b7
Successfully installed bundler-2.0.1
1 gem installed
Removing intermediate container 3ea22bf774b7
 ---> 5f0ce919f381
Step 8/9 : RUN bundle install
 ---> Running in e854bd94d444
Warning: the running version of Bundler (1.16.6) is older than the version that created the lockfile (1.17.3). We suggest you upgrade to the latest version of Bundler by running `gem install bundler`.
The dependency tzinfo-data (>= 0) will be unused by any of the platforms Bundler is installing for. Bundler is installing for ruby but the dependency is only for x86-mingw32, x86-mswin32, x64-mingw32, java. To add those platforms to the bundle, run `bundle lock --add-platform x86-mingw32 x86-mswin32 x64-mingw32 java`.
Fetching gem metadata from https://rubygems.org/............
Fetching rake 12.3.2
Installing rake 12.3.2
Fetching concurrent-ruby 1.1.5
Installing concurrent-ruby 1.1.5
Fetching i18n 1.6.0
Installing i18n 1.6.0
Fetching minitest 5.11.3
Installing minitest 5.11.3
Fetching thread_safe 0.3.6
Installing thread_safe 0.3.6
Fetching tzinfo 1.2.5
Installing tzinfo 1.2.5
Fetching activesupport 5.2.2.1
Installing activesupport 5.2.2.1
Fetching builder 3.2.3
Installing builder 3.2.3
Fetching erubi 1.8.0
Installing erubi 1.8.0
Fetching mini_portile2 2.4.0
Installing mini_portile2 2.4.0
Fetching nokogiri 1.10.1
Installing nokogiri 1.10.1 with native extensions
Fetching rails-dom-testing 2.0.3
Installing rails-dom-testing 2.0.3
Fetching crass 1.0.4
Installing crass 1.0.4
Fetching loofah 2.2.3
Installing loofah 2.2.3
Fetching rails-html-sanitizer 1.0.4
Installing rails-html-sanitizer 1.0.4
Fetching actionview 5.2.2.1
Installing actionview 5.2.2.1
Fetching rack 2.0.6
Installing rack 2.0.6
Fetching rack-test 1.1.0
Installing rack-test 1.1.0
Fetching actionpack 5.2.2.1
Installing actionpack 5.2.2.1
Fetching nio4r 2.3.1
Installing nio4r 2.3.1 with native extensions
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Fetching mini_mime 1.0.1
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Fetching activemodel 5.2.2.1
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Fetching arel 9.0.0
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Fetching activerecord 5.2.2.1
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Fetching mimemagic 0.3.3
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Fetching marcel 0.3.3
Installing marcel 0.3.3
Fetching activestorage 5.2.2.1
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Fetching public_suffix 3.0.3
Installing public_suffix 3.0.3
Fetching addressable 2.6.0
Installing addressable 2.6.0
Fetching io-like 0.3.0
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Fetching bindex 0.5.0
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Fetching msgpack 1.2.9
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Fetching bootsnap 1.4.1
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Fetching bson 4.4.2
Installing bson 4.4.2 with native extensions
Using bundler 1.16.6
Fetching byebug 11.0.1
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Fetching regexp_parser 1.3.0
Installing regexp_parser 1.3.0
Fetching xpath 3.2.0
Installing xpath 3.2.0
Fetching capybara 3.15.0
Installing capybara 3.15.0
Fetching ffi 1.10.0
Installing ffi 1.10.0 with native extensions
Fetching childprocess 0.9.0
Installing childprocess 0.9.0
Fetching chromedriver-helper 2.1.0
Installing chromedriver-helper 2.1.0
Fetching coffee-script-source 1.12.2
Installing coffee-script-source 1.12.2
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Installing execjs 2.7.0
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Installing coffee-script 2.4.1
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Installing method_source 0.9.2
Fetching thor 0.20.3
Installing thor 0.20.3
Fetching railties 5.2.2.1
Installing railties 5.2.2.1
Fetching coffee-rails 4.2.2
Installing coffee-rails 4.2.2
Fetching multi_json 1.13.1
Installing multi_json 1.13.1
Fetching jbuilder 2.8.0
Installing jbuilder 2.8.0
Fetching rb-fsevent 0.10.3
Installing rb-fsevent 0.10.3
Fetching rb-inotify 0.10.0
Installing rb-inotify 0.10.0
Fetching ruby_dep 1.5.0
Installing ruby_dep 1.5.0
Fetching listen 3.1.5
Installing listen 3.1.5
Fetching mongo 2.7.1
Installing mongo 2.7.1
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Installing mongoid 7.0.2
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Installing puma 3.12.1 with native extensions
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Installing sprockets 3.7.2
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Fetching rails 5.2.2.1
Installing rails 5.2.2.1
Fetching rubyzip 1.2.2
Installing rubyzip 1.2.2
Fetching sass-listen 4.0.0
Installing sass-listen 4.0.0
Fetching sass 3.7.3
Installing sass 3.7.3
Fetching tilt 2.0.9
Installing tilt 2.0.9
Fetching sass-rails 5.0.7
Installing sass-rails 5.0.7
Fetching selenium-webdriver 3.141.0
Installing selenium-webdriver 3.141.0
Fetching spring 2.0.2
Installing spring 2.0.2
Fetching spring-watcher-listen 2.0.1
Installing spring-watcher-listen 2.0.1
Fetching turbolinks-source 5.2.0
Installing turbolinks-source 5.2.0
Fetching turbolinks 5.2.0
Installing turbolinks 5.2.0
Fetching uglifier 4.1.20
Installing uglifier 4.1.20
Fetching web-console 3.7.0
Installing web-console 3.7.0
Bundle complete! 18 Gemfile dependencies, 81 gems now installed.
Bundled gems are installed into `/usr/local/bundle`
Post-install message from i18n:

HEADS UP! i18n 1.1 changed fallbacks to exclude default locale.
But that may break your application.

Please check your Rails app for 'config.i18n.fallbacks = true'.
If you're using I18n (>= 1.1.0) and Rails (< 5.2.2), this should be
'config.i18n.fallbacks = [I18n.default_locale]'.
If not, fallbacks will be broken in your app by I18n 1.1.x.

For more info see:
https://github.com/svenfuchs/i18n/releases/tag/v1.1.0

Post-install message from sass:

Ruby Sass is deprecated and will be unmaintained as of 26 March 2019.

* If you use Sass as a command-line tool, we recommend using Dart Sass, the new
  primary implementation: https://sass-lang.com/install

* If you use Sass as a plug-in for a Ruby web framework, we recommend using the
  sassc gem: https://github.com/sass/sassc-ruby#readme

* For more details, please refer to the Sass blog:
  http://sass.logdown.com/posts/7081811

Removing intermediate container e854bd94d444
 ---> 6c37b33e09a5
Step 9/9 : COPY . /app
 ---> cf7322d43f1f
Successfully built cf7322d43f1f
Successfully tagged mongoid_sample_web:latest

結果

無事に起動しました！

image.png

Docker上でRailsがMongoDBで動いていることも確認！

image.png

気付いたこと

今回のエラーは最初に docker-compose build をせず、直接 docker-compose run web bundle install を実行した状態でサーバーを起動しようとしたところ起こりました...
そもそも docker-compose.yml に bundle install コマンドを書いていたので、最初から docker-compose build を一発実行すれば変なキャッシュが残ってインストール出来ない問題もなかったのでは？そんな風に思います。
他の解決法があるのか詳しくは分からないですが、こうしたキャッシュ絡みのインストールトラブルの際は docker-compose build --no-cache でイケそうということがわかったのでひとまずよかった。