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Start by preserving the complete error, then identify which layer failed: a native extension, dependency resolution, Ruby or Bundler version selection, TLS, or the install path. Run the checks from the Rails application directory, keep Gemfile.lock intact, and make the smallest change that addresses the evidence. Most native-extension failures on Ubuntu are fixed by installing the compiler toolchain and the development headers named in mkmf.log; version and dependency failures require a deliberate change to the runtime or dependency constraints instead.
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What bundle install actually does
Bundler reads the Rails application’s Gemfile, resolves the declared gems and their dependencies, and installs the resulting set. If Gemfile.lock is present and the Gemfile has not changed in a way that requires re-resolution, Bundler uses the versions recorded in that lockfile rather than selecting an entirely new set. That distinction matters: a failed install is usually an environment or prerequisite problem, not a reason to erase the lockfile.
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| File or command | What it tells you | Why it matters during a failure |
|---|---|---|
Gemfile |
Direct dependency declarations and version constraints | A changed constraint can trigger a new resolution |
Gemfile.lock |
The resolved versions and dependency graph | Preserves the known-good set across machines; keep it under version control |
bundle check |
Whether the requirements are installed | Separates a missing installation from a resolution problem |
bundle env |
Bundler, Ruby and project context | Provides the runtime details needed to reproduce the failure |
bundle config list |
Effective Bundler settings | Reveals custom paths, deployment mode and excluded groups |
Preserve evidence before changing anything
Run the command from the directory containing the Rails app’s Gemfile. Save the entire terminal output, not just the final line. The gem name, Ruby version, Bundler version, compiler message and any printed path to mkmf.log determine the correct repair.
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- Record the runtime. Run
ruby -vandwhich ruby. The first command reports the version; the second shows which executable is actually being used. - Record Bundler and its context. Run
bundle -vandbundle env. This catches a shell that is using a different Ruby or Bundler than the one expected by the project. - Check the current installation state. Run
bundle check. Its result indicates whether required gems are already installed, but it does not replace diagnosis of a compiler or TLS error. - Inspect project constraints. Read the Ruby requirement in the
Gemfile, check.ruby-versionif present, and note the Bundler version recorded in the lockfile. Compare all of them with the commands above. - Keep the lockfile. Do not remove
Gemfile.lockas a first response. Make a backup or commit unrelated edits before experimenting so that the original dependency state remains recoverable.
These checks also prevent a common misdiagnosis: running bundle install with a system Ruby when the project was created with a version-manager Ruby, or running it from a parent directory that contains a different Gemfile.
Fix native-extension and compiler failures
Messages such as Failed to build gem native extension, extconf.rb failed, Could not create Makefile, or a missing header usually mean that a gem must compile C or C++ code and the operating system lacks a required tool. RubyGems’ troubleshooting guidance says, “The most common cause is a missing compiler toolchain.”
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The failed build prints the path to mkmf.log. Open that file and look for the first missing command, header, library or configuration test. The final Bundler error is often only a summary; mkmf.log identifies the actual prerequisite. For example, an error naming a SQLite, PostgreSQL, libxml2, libxslt or OpenSSL header points to that library’s Ubuntu development package, not to an arbitrary collection of packages.
Install Ubuntu’s basic build prerequisites
For Ubuntu’s packaged Ruby, install the compiler toolchain and Ruby headers, then retry:
sudo apt-get update
sudo apt-get install build-essential ruby-dev
bundle installbuild-essential supplies the standard compiler and build utilities. ruby-dev supplies headers needed when the Ruby interpreter came from Ubuntu’s distribution packages. If Ruby was compiled or installed by a version manager, that Ruby may already include its own headers; installing ruby-dev is not a substitute for selecting the correct version-manager environment.
Install only the library named by the log
If the log reports a missing system header or library, install the matching Ubuntu -dev package for that dependency and the Ubuntu release in use. Typical families include development packages for SQLite, PostgreSQL, libxml2/libxslt and libssl, but the exact package name depends on the gem and release. Confirm the name from the log and the gem’s installation documentation instead of adding unrelated packages.
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| Symptom in the build output | Likely next check | Repair approach |
|---|---|---|
Could not create Makefile or compiler not found |
Whether build-essential is installed |
Install the toolchain, then rerun the same command |
Ruby header such as ruby.h is missing |
How Ruby was installed | Install ruby-dev for distribution Ruby, or select/install headers for the version-manager Ruby |
| Database or XML header is missing | The exact header named in mkmf.log |
Install the corresponding Ubuntu library development package |
| OpenSSL header or library cannot be found | OpenSSL development files and the selected Ruby’s build configuration | Install the required development package or rebuild/select Ruby with a usable OpenSSL |
After installing a prerequisite, rerun bundle install without changing gem versions. If the failure moves to a different missing header, repeat the same evidence-based process. If the log instead shows an incompatible compiler flag or Ruby API, stop adding packages and investigate the gem version against the selected Ruby.
Resolve “could not find compatible versions” errors
A dependency-resolution failure is a requirements chain, not a single bad gem. Read the error from the top-level gem through each constraint until you find the incompatible pair. One gem may require an older dependency while another requires a newer release, or the project may constrain a gem more tightly than its current Ruby supports.
Update the gem you intentionally changed
If you edited one dependency, update only that gem first:
bundle update GEMReplace GEM with the gem whose constraint or version you changed. This keeps unrelated locked versions in place and makes the resulting lockfile diff understandable.
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Use conservative updating for indirect dependencies
When the direct gem must move but its indirect dependencies should remain locked where possible, use:
bundle update GEM --conservativeConservative updating limits collateral upgrades. It is useful when a security or feature change targets one gem but the application has not been tested against a wholesale dependency refresh.
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Change constraints deliberately
Loosen a version constraint only when the requirement chain demonstrates that the current constraint prevents a compatible set. Record why the constraint changed and review the resulting lockfile diff. Do not respond to one conflict by upgrading Rails, Ruby and every gem at once; changing several variables removes the evidence needed to identify the incompatible requirement.
Run bundle outdated when you need to see stale dependencies, but treat its output as an inventory, not an instruction to upgrade everything. A package can be outdated and still be the correct locked version for the application’s Ruby and Rails release.
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Before altering dependencies, verify that the project is running the Ruby it expects. Compare the Ruby requirement in the Gemfile and .ruby-version with ruby -v and which ruby. A shell can silently select a system executable even when another Ruby is installed.
Select the intended Ruby first
Use the project’s established Ruby version manager or installation method to select the version named by the project. Rails’ Bundler guidance recommends a dependable Ruby installation method when switching between Ruby versions. After selecting Ruby, open a new shell if the manager requires it, then rerun ruby -v and which ruby to confirm the change.
Match Bundler to the project
Compare bundle -v with the Bundler version recorded in Gemfile.lock and any project setup documentation. Install or invoke the compatible Bundler version only after the intended Ruby is active. A Bundler mismatch can alter lockfile handling or reject dependencies even when the gem declarations themselves are valid.
Do not “fix” a runtime mismatch by deleting the lockfile. First make the executable and Bundler match the project, then run bundle install against the existing lockfile. If the project genuinely needs a Ruby upgrade, treat that as a planned compatibility change: update the Ruby requirement, test the application, and review dependency changes separately.
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Repair SSL, certificate and rubygems.org connection errors
When the output mentions certificates, TLS, or an inability to connect to rubygems.org, run Bundler’s diagnostic:
bundle doctor sslThis check examines Ruby’s OpenSSL setup, trusted CA certificates and the TLS connection to rubygems.org. Follow the specific issue it reports: repair the CA bundle, OpenSSL installation, Ruby build or proxy configuration named by the diagnostic, then retry the original install.
Corporate proxies can replace certificates or require explicit proxy settings. Verify the proxy’s CA certificate is trusted by the Ruby process, not merely by a browser. A successful browser connection does not prove that the Ruby executable selected by which ruby has the same trust store.
Do not disable certificate verification as a permanent workaround. It removes the protection that TLS is supposed to provide and can conceal a damaged or intercepted connection. If the diagnostic cannot identify the cause, preserve its output along with bundle env and investigate the OpenSSL and CA paths used by the active Ruby.
Handle deployment mode, groups, paths and permissions
Some failures occur after dependency resolution because Bundler is installing to a path the current user cannot write, or because deployment settings differ from development settings. Check the effective configuration:
bundle config listDeployment path
In deployment mode, Bundler installs into vendor/bundle unless another path is configured. Confirm that the application user owns the path and that the filesystem has space. Run the command as the intended application user rather than alternating between an unprivileged account and sudo; mixed ownership commonly creates a directory that later commands cannot update.
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Groups and the without setting
Bundler can exclude installation groups, such as development or test, through its group settings. Excluding a group changes what is installed locally, but Bundler still resolves the full dependency set when creating the lockfile. Therefore, an excluded gem can still participate in a resolution conflict even though it will not be installed on that host.
Inspect the configured groups and path rather than assuming the command-line environment is clean. Remove an obsolete setting only when you know why it was added, then retry with the project’s intended deployment configuration.
Retry with the smallest possible change
Once the evidence identifies the cause, correct only that cause and rerun the same install:
- For a compiler failure, install the missing toolchain or exact development package named by
mkmf.log. - For a version mismatch, select the project’s Ruby and compatible Bundler before touching the Gemfile.
- For a dependency conflict, update the gem that changed, using
--conservativewhen indirect versions should remain locked. - For TLS, repair the CA, OpenSSL or proxy problem identified by
bundle doctor ssl. - For deployment failures, correct the configured path, group selection or ownership and run as the intended user.
Run bundle install again and compare its output with the original. With an unchanged Gemfile and a valid lockfile, the expected operation is installation of the locked gems, not a broad dependency upgrade. Finish by running bundle check; in a Rails project, follow the application’s normal test or boot command to verify that the repaired environment works beyond installation.
Choose between competing repairs
When more than one fix appears possible, prefer the option that changes the least while preserving reproducibility.
Quick Recap
| Repair option | Preserves the committed lockfile? | Changes Ruby runtime? | Typical risk | Use it when |
|---|---|---|---|---|
Install the missing compiler or named -dev package |
Yes | No | Low; adds an operating-system prerequisite | mkmf.log names a missing tool, header or library |
| Select the project’s existing Ruby and Bundler | Yes | Uses the intended runtime | Low if the versions are documented | ruby -v, .ruby-version or lockfile metadata disagree |
bundle update GEM --conservative |
No; changes a focused portion | Usually no | Moderate; the selected gem and allowed dependents move | A deliberate Gemfile change created a requirement conflict |
| Loosen a Gemfile constraint | No; requires a new resolution | Usually no | Moderate to high; a wider version range may alter behavior | The requirement chain proves the current constraint is too narrow |
Delete Gemfile.lock |
No | Not necessarily | High; every dependency may be re-resolved | Only as a planned, reviewed regeneration—not as first-line troubleshooting |
| Disable TLS verification | Yes | No | Unacceptable security exposure | Do not use as a permanent repair |
Quick symptom-to-action checklist
- “Failed to build gem native extension”: open the printed
mkmf.logpath; installbuild-essentialand, for Ubuntu’s packaged Ruby,ruby-dev; then install only the additional library development package the log names. - “Could not find compatible versions”: trace the requirement chain; update the gem you changed; use
--conservativefor a focused update; keep the lockfile. - Ruby syntax or required-version error: compare the Gemfile requirement and
.ruby-versionwithruby -vandwhich ruby; select the intended Ruby before changing gems. - Bundler version complaint: compare
bundle -vwith the lockfile’s Bundler metadata and invoke a compatible version. - Certificate or TLS failure: run
bundle doctor ssl; repair the CA, OpenSSL or proxy issue it identifies; do not bypass verification. - Permission or missing-path failure in deployment: inspect
bundle config list, checkvendor/bundleor the configured path, and run as the application user. - Unclear state: save the original output, run
bundle envandbundle check, and avoid deletingGemfile.lockuntil the cause is understood.
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