Troubleshooting Claude Code: A Deep Dive into NPM Package Management

By Thanh Phong Le July 30, 2025

The Mystery of the Missing Command

When encountering a command not found error in Linux, the natural assumption might be that the software isn't installed. However, as this troubleshooting journey reveals, the reality can be far more complex and educational.

Initial Symptoms

$ claude
claude: command not found

Diagnostic Commands That Revealed the Truth

1. Checking Installation Existence

# First instinct: Is it installed at all?
$ which claude || echo "Not in PATH"
$ ls -la ~/.local/bin/claude 2>/dev/null || echo "Not in ~/.local/bin"
$ ls -la /usr/local/bin/claude 2>/dev/null || echo "Not in /usr/local/bin"

Finding: No claude executable found in standard locations.

2. Discovering NPM Installation Issues

# Attempting reinstallation revealed deeper problems
$ npm install -g @anthropic-ai/claude-code
npm error code ENOTEMPTY
npm error syscall rename

Finding: NPM's atomic installation process was blocked by non-empty directories.

3. Investigating the Corrupted Installation

# What's actually in the installation directory?
$ ls -la /path/to/node_modules/@anthropic-ai/claude-code
total 12
drwxr-xr-x 3 lenovo lenovo 4096 Jul 30 11:18 node_modules

Finding: Only an empty node_modules subdirectory existed - no actual package files!

4. Uncovering the Failed Dependency Installation

# Diving deeper into the mysterious node_modules
$ find /path/to/claude-code/node_modules -type f -ls
10273 -rw-r--r-- 1 lenovo lenovo 10273 Jul 30 11:18 .../LICENSE
    0 -rw-r--r-- 1 lenovo lenovo     0 Jul 30 11:18 .../package.json

Finding: Sharp image processing library installation failed mid-process, leaving only a LICENSE file and empty package.json.

5. Discovering the Hidden Working Installation

# NPM's temporary directories revealed a surprise
$ ls -la /path/to/node_modules/@anthropic-ai/
drwxr-xr-x 4 lenovo lenovo 4096 Jul 30 10:50 .claude-code-OJdXb3xe

Finding: A complete, functional installation was hidden in a temporary directory!

The Root Causes

The investigation revealed a perfect storm of NPM package management challenges:

1. Interrupted Atomic Operations: NPM's safety mechanism of renaming directories during updates had failed, leaving both temporary and corrupted directories
2. Broken Symbolic Links: The command-line interface existed but wasn't linked to the system PATH
3. Partial Dependency Installation: The Sharp library's binary download was interrupted, blocking NPM's safety checks
4. IDE Integration Confusion: IntelliJ IDEA's plugin couldn't locate the CLI tool due to the non-standard installation state

The Solution Path

Quick Fix (Recovering Existing Installation)

# Create symlink to the hidden but functional installation
$ ln -sf /path/to/.claude-code-OJdXb3xe/cli.js /path/to/bin/claude

Clean Reinstallation (Recommended)

# 1. Remove all traces of corrupted installation
$ rm -rf /path/to/node_modules/@anthropic-ai/claude-code
$ rm -rf /path/to/node_modules/@anthropic-ai/.claude-code-*
$ rm -f /path/to/bin/.claude-*

# 2. Fresh installation
$ npm install -g @anthropic-ai/claude-code

# 3. Verify success
$ which claude && claude --version

Key Learnings for Node.js Architects

This troubleshooting experience illuminates several critical aspects of Node.js ecosystem management:

• NPM's Atomic Operations: Understanding how NPM uses temporary directories and renames to ensure safe updates
• Symbolic Link Management: Global NPM packages rely on symlinks in PATH-accessible directories
• Dependency Complexity: Native dependencies like Sharp can fail differently than pure JavaScript packages
• Configuration Preservation: User data in ~/.claude survived the corrupted installation, demonstrating good separation of concerns

The Architectural Insight

Modern development tools often employ a two-tier architecture:

• CLI Core: Installed via package managers, provides the actual functionality
• IDE Plugins: Lightweight integrations that communicate with the CLI tool

This separation enables consistent functionality across different development environments while maintaining a single source of truth for the core logic.

This investigation transformed a simple "command not found" error into a masterclass in Node.js package management, demonstrating the value of systematic debugging and deep system understanding.

If you enjoyed this article, you can also find it published on LinkedIn and Medium.