mavaddat/brew_common_issues.md

## brew_common_issues.md

      
    Raw
  

              brew_common_issues.md
            
          
    Common Issues with Homebrew

This is a list of commonly encountered problems with packages on Homebrew, known issues, and their
solutions. 
brew complains about absence of “Command Line Tools”

You need to have the Xcode Command Line Utilities installed (and
updated): run xcode-select --install in the terminal.
Ruby: bad interpreter: /usr/bin/ruby^M: no such file or directory

You cloned with git, and your Git configuration is set to use Windows
line endings. See this page:
https://help.github.com/articles/dealing-with-line-endings
Ruby: bad interpreter: /usr/bin/ruby

You don’t have a /usr/bin/ruby or it is not executable. It’s not
recommended to let this persist; you’d be surprised how many .apps,
tools and scripts expect your macOS-provided files and directories to be
unmodified since macOS was installed.
brew update complains about untracked working tree files

After running brew update, you receive a Git error warning about
untracked files or local changes that would be overwritten by a checkout
or merge, followed by a list of files inside your Homebrew installation.
This is caused by an old bug in in the update code that has long since
been fixed. However, the nature of the bug requires that you do the
following:
cd "$(brew --repository)"
git reset --hard FETCH_HEAD

If brew doctor still complains about uncommitted modifications, also
run this command:
cd "$(brew --repository)/Library"
git clean -fd

launchctl refuses to load launchd plist files

When trying to load a plist file into launchctl, you receive an error
that resembles
Bug: launchctl.c:2325 (23930):13: (dbfd = open(g_job_overrides_db_path, [...]
launch_msg(): Socket is not connected

or
Could not open job overrides database at: /private/var/db/launchd.db/com.apple.launchd/overrides.plist: 13: Permission denied
launch_msg(): Socket is not connected

These are likely due to one of four issues:

You are using iTerm. The solution is to use Terminal.app when
interacting with launchctl.
You are using a terminal multiplexer such as tmux or screen. You
should interact with launchctl from a separate Terminal.app shell.
You are attempting to run launchctl while logged in remotely. You
should enable screen sharing on the remote machine and issue the
command using Terminal.app running on that machine.
You are su‘ed as a different user.

brew upgrade errors out

When running brew upgrade, you see something like this:
$ brew upgrade
Error: undefined method `include?' for nil:NilClass
Please report this bug:
    https://docs.brew.sh/Troubleshooting
/usr/local/Library/Homebrew/formula.rb:393:in `canonical_name'
/usr/local/Library/Homebrew/formula.rb:425:in `factory'
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7:in `map'
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7
/usr/local/bin/brew:46:in `require'
/usr/local/bin/brew:46:in `require?'
/usr/local/bin/brew:79

This happens because an old version of the upgrade command is hanging
around for some reason. The fix:
cd "$(brew --repository)/Library/Contributions/examples"
git clean -n # if this doesn't list anything that you want to keep, then
git clean -f # this will remove untracked files

Python: easy-install.pth cannot be linked

Warning: Could not link <formula>. Unlinking...
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
You can try again using `brew link <formula>'

Possible conflicting files are:
/usr/local/lib/python2.7/site-packages/site.py
/usr/local/lib/python2.7/site-packages/easy-install.pth
==> Could not symlink file: /homebrew/Cellar/<formula>/<version>/lib/python2.7/site-packages/site.py
Target /usr/local/lib/python2.7/site-packages/site.py already exists. You may need to delete it.
To force the link and overwrite all other conflicting files, do:
  brew link --overwrite formula_name

To list all files that would be deleted:
  brew link --overwrite --dry-run formula_name

Don’t follow the advice here but fix by using
Language::Python.setup_install_args in the formula as described in
Python for Formula Authors.
Upgrading macOS

Upgrading macOS can cause errors like the following:

dyld: Library not loaded: /usr/local/opt/icu4c/lib/libicui18n.54.dylib
configure: error: Cannot find libz

Following a macOS upgrade it may be necessary to reinstall the Xcode
Command Line Tools and brew upgrade all installed formula:
xcode-select --install
brew upgrade

Other local issues

If your Homebrew installation gets messed up (and fixing the issues
found by brew doctor doesn’t solve the problem), reinstalling Homebrew
may help to reset to a normal state. To easily reinstall Homebrew, use
Homebrew Bundle to
automatically restore your installed formulae and casks. To do so, run
brew bundle dump,
uninstall,
reinstall and run
brew bundle install.

  
## fixBrews.sh
#! /bin/bash
# This script will fix the Homebrew installation on a Mac
# $1 is the broken executable
# $2 is the number of re-tries

# check if any brews have problems
BREW_PROBLEMS=$(brew doctor | grep -c "Your Homebrew is not working")
# if there are problems, fix them
if [ $BREW_PROBLEMS -gt 0 ]; then
  echo "Fixing Homebrew..."
  brew doctor
  brew update
  brew upgrade
  brew cleanup
  brew cask cleanup

  # check if any brews have problems
  BREW_PROBLEMS=$(brew doctor | grep -c "Your Homebrew is not working")
  # if we have retries, then re-run the script
    if [ $BREW_PROBLEMS -gt 0 ]; then
        if [ $2 -gt 0 ]; then
            echo "Retrying Homebrew fix..."
            bash $0 $1 $(( $2 - 1 ))
        else
            echo "Failed to fix Homebrew"
            exit 1
        fi
    fi
else
  echo "Homebrew is OK."
fi

# Re-install $1
if [ -n "$1" ]; then
  echo "Re-installing $1..."
  # Remove the broken executable
  brew uninstall $1
  # Re-install the broken executable
  brew install $1
fi

# if the exit code is not 0, re-run the script
if [ $? -ne 0 ]; then
  if [ -n "$2" ]; then
    if [ $2 -gt 0 ]; then
      echo "Re-trying $0..."
      bash $0 $1 $(($2 - 1))
    else
      echo "Failed to fix $1."
    fi
  fi
fi

## fixBrokenRuby.sh
#! /bin/bash
# Check if Ruby installed via Snap
sys_ruby=`which ruby`
if [ "$sys_ruby" = "/snap/bin/ruby" ]; then
  echo "Ruby is installed via Snap"
  # check if snaps are broken
  python3 ./fixSnaps.py ruby 3  # retries 3 times
# Check if Ruby installed via Homebrew
elif [ "$sys_ruby" = "/usr/local/bin/ruby" ]; then
  echo "Ruby is installed via Homebrew"
  # check if brews are broken
  python3 ./fixBrews.py ruby 3  # retries 3 times
fi
# Assume path problem
./reorderPathForExe.sh

## fixSnaps.py
#! /usr/bin/python3
import subprocess
import os
import sys

# the executable that is not working
BROKE_EXE = sys.argv[1] if len(sys.argv) > 1 else None

# how many times to re-try
RETRY_COUNT = sys.argv[2] if len(sys.argv) > 2 else 1


def get_broken_snaps_or_exit(exe=None) -> list:
    """
    Provides a list of the broken snaps
    """
    # If the executable is not broken, exit
    if (
        exe and
        subprocess.call([exe, "--version"]) * subprocess.call([exe, "-v"]) == 0
    ):
        print("{} is not broken".format(BROKE_EXE))
        exit(0)
    raw_snap_out = None
    raw_snap_out = subprocess.check_output(["snap", "list"])
    snap_out = raw_snap_out.decode('utf-8').splitlines()
    # Return list where 'Notes' field says "broken"
    broken = [x for x in snap_out[1:] if "broken" in x]
    if len(broken) == 0:
        print("No broken snaps found")
        exit(0)
    return broken


# Get the list of broken snaps
broken_snaps = get_broken_snaps_or_exit(BROKE_EXE)


def _fix_snaps_or_exit(snaps: list) -> None:
    # run sudo snap remove on each broken snap
    result = None
    for snap in snaps:
        snap_name = snap.split()[0]
        print("Removing broken snap: %s" % snap_name)
        result = subprocess.run(["sudo", "snap", "remove", snap_name])
        if result.returncode != 0:
            print("Error removing snap: %s" % snap_name)
            exit(1)
        # add a sleep to give the snap a chance to finish
        subprocess.run(["sleep", "1"])
    # run sudo snap install on each removed snap
    for snap in snaps:
        # re-add the snap
        print("Adding snap: %s" % snap_name)
        # check if we need "--classic" flag
        has_classic = "classic" in subprocess.check_output(
                ["snap", "info", snap_name]
            ).stdout.decode('utf-8')
        if has_classic:
            result = subprocess.run(
                ["sudo", "snap", "install", snap_name, "--classic"]
            )
        else:
            result = subprocess.run(["sudo", "snap", "install", snap_name])
        if result.returncode != 0:
            print("Error adding snap: %s" % snap_name)
            exit(1)
        # add a sleep to give the snap a chance to finish
        subprocess.run(["sleep", "1"])


def fix_snaps_or_exit(snaps: list) -> None:
    # check if we have root access
    if os.geteuid() != 0:
        print("Run this script as root to fix broken snaps")
        exit(1)
    # get the core snap
    core_snaps = [x for x in snaps if "canonical" in x]
    _fix_snaps_or_exit(core_snaps)
    # get the other snaps
    other_snaps = [x for x in snaps if "canonical" not in x]
    _fix_snaps_or_exit(other_snaps)


# Fix the broken snaps
fix_snaps_or_exit(broken_snaps)

# if we still have broken snaps, we need to retry
if len(get_broken_snaps_or_exit(BROKE_EXE)) > 0 and RETRY_COUNT > 1:
    print("Retrying to fix broken snaps")
    # run the script again
    subprocess.run(["./fixSnaps.py", BROKE_EXE, str(RETRY_COUNT - 1)])
else:
    print("Failed to fix broken snaps")
    exit(1)

## reorderPathForExe.sh
#! /bin/bash

#$1 is the executable that isn't working correctly

# This script is used to modify the path priority for
# the executable that is not working correctly

# Store the output of `which` application for the executable
execPaths=($(which -a $1))
execPath="" #  this will be the path that the user selects to prioritize

# if the argument is not found, exit
if [ $? -ne 0 ]; then
    echo "Error: $1 not found"
    exit 1
fi
# if there is only one path, then there are no alternatives, nothing to do
if [ ${#execPaths[@]} -eq 1 ]; then
	echo "You have only one path to determine $1 ('${execPaths[0]}')"
	exit 1
elif [ ${#execPaths[@]} -eq 2 ]; then
	echo -e "\e[0m\e[36mCurrently, '${execPaths[0]}' is the priority for $1."
	echo -e "Would you rather prioritize '${execPaths[1]}' instead (y/N)?\e[0m"
	read answer
	if [ "$answer" != "y" ]; then
		exit 1
	fi
	execPath=${execPaths[1]}
else
	# tell the user what paths are determining the executable
	echo -e "\e[1;32mThe following paths determine which $1:"
	#loop through the paths
	for execPath in ${execPaths[@]}; do
		echo "$execPath"
	done
	PS3="Please enter the number of the path you would like to prioritize: "
	echo -e "\e[0m\e[36mWhich path do you want to \e[0m\e[36m\e[1mprioritize?\e[0m\e[36m"
	select execPath in ${execPaths[@]:1}; do
		# if the user selects a path, break out of the loop
		if [ $? -eq 0 ]; then
			break
		fi
	done
fi

# calculate unintended consequences
affected=($(ls $execPath))
bffected=( $(ls ${execPaths[0]}) )
# calculate set intersection of `affected` and `bffected`
common=($(comm -12 <(printf '%s\n' "${affected[@]}" | LC_ALL=C sort) <(printf '%s\n' "${bffected[@]}" | LC_ALL=C sort)))
# warn about consequences
echo -e "\e[31mWarning: Path re-ordering will also affect the following files:"
for file in $common; do
    echo "$file"
done

echo -e "Do you want to continue? (y/N)\e[0m"
read answer
if [ "$answer" != "y" ]; then
    exit 1
fi

# reorder the system path to prioritize the selected path
#   first, remove the path from the system path
PATH=$(echo $PATH | sed -e "s;:$exePath;;")
#   then, add the path to the front of the system path
PATH="$exePath:$PATH"

# ask if the user wants to save the new path
echo "Do you want to save the new path to your bash profile? (y/N)"
read answer
if [ "$answer" != "y" ]; then
    echo "Before export,"
    declareNewPath $1
    export PATH=$PATH
    echo "After export (which is not included in your bash profile),"
    declareNewPath $1
    exit 0
fi

# save the new path to the bash profile
echo "export PATH=\"$PATH\"" >> ~/.bash_profile
declareNewPath $1
function declareNewPath() {
    # tell the user what the new path is that determines the executable
    echo "System declares that new path to $1 is:"
    echo "$( which $1 )"
    exit 0
}
	#! /bin/bash
	# This script will fix the Homebrew installation on a Mac
	# $1 is the broken executable
	# $2 is the number of re-tries

	# check if any brews have problems
	BREW_PROBLEMS=$(brew doctor \| grep -c "Your Homebrew is not working")
	# if there are problems, fix them
	if [ $BREW_PROBLEMS -gt 0 ]; then
	echo "Fixing Homebrew..."
	brew doctor
	brew update
	brew upgrade
	brew cleanup
	brew cask cleanup

	# check if any brews have problems
	BREW_PROBLEMS=$(brew doctor \| grep -c "Your Homebrew is not working")
	# if we have retries, then re-run the script
	if [ $BREW_PROBLEMS -gt 0 ]; then
	if [ $2 -gt 0 ]; then
	echo "Retrying Homebrew fix..."
	bash $0 $1 $(( $2 - 1 ))
	else
	echo "Failed to fix Homebrew"
	exit 1
	fi
	fi
	else
	echo "Homebrew is OK."
	fi

	# Re-install $1
	if [ -n "$1" ]; then
	echo "Re-installing $1..."
	# Remove the broken executable
	brew uninstall $1
	# Re-install the broken executable
	brew install $1
	fi

	# if the exit code is not 0, re-run the script
	if [ $? -ne 0 ]; then
	if [ -n "$2" ]; then
	if [ $2 -gt 0 ]; then
	echo "Re-trying $0..."
	bash $0 $1 $(($2 - 1))
	else
	echo "Failed to fix $1."
	fi
	fi
	fi
	#! /bin/bash
	# Check if Ruby installed via Snap
	sys_ruby=`which ruby`
	if [ "$sys_ruby" = "/snap/bin/ruby" ]; then
	echo "Ruby is installed via Snap"
	# check if snaps are broken
	python3 ./fixSnaps.py ruby 3 # retries 3 times
	# Check if Ruby installed via Homebrew
	elif [ "$sys_ruby" = "/usr/local/bin/ruby" ]; then
	echo "Ruby is installed via Homebrew"
	# check if brews are broken
	python3 ./fixBrews.py ruby 3 # retries 3 times
	fi
	# Assume path problem
	./reorderPathForExe.sh
	#! /usr/bin/python3
	import subprocess
	import os
	import sys

	# the executable that is not working
	BROKE_EXE = sys.argv[1] if len(sys.argv) > 1 else None

	# how many times to re-try
	RETRY_COUNT = sys.argv[2] if len(sys.argv) > 2 else 1


	def get_broken_snaps_or_exit(exe=None) -> list:
	"""
	Provides a list of the broken snaps
	"""
	# If the executable is not broken, exit
	if (
	exe and
	subprocess.call([exe, "--version"]) * subprocess.call([exe, "-v"]) == 0
	):
	print("{} is not broken".format(BROKE_EXE))
	exit(0)
	raw_snap_out = None
	raw_snap_out = subprocess.check_output(["snap", "list"])
	snap_out = raw_snap_out.decode('utf-8').splitlines()
	# Return list where 'Notes' field says "broken"
	broken = [x for x in snap_out[1:] if "broken" in x]
	if len(broken) == 0:
	print("No broken snaps found")
	exit(0)
	return broken


	# Get the list of broken snaps
	broken_snaps = get_broken_snaps_or_exit(BROKE_EXE)


	def _fix_snaps_or_exit(snaps: list) -> None:
	# run sudo snap remove on each broken snap
	result = None
	for snap in snaps:
	snap_name = snap.split()[0]
	print("Removing broken snap: %s" % snap_name)
	result = subprocess.run(["sudo", "snap", "remove", snap_name])
	if result.returncode != 0:
	print("Error removing snap: %s" % snap_name)
	exit(1)
	# add a sleep to give the snap a chance to finish
	subprocess.run(["sleep", "1"])
	# run sudo snap install on each removed snap
	for snap in snaps:
	# re-add the snap
	print("Adding snap: %s" % snap_name)
	# check if we need "--classic" flag
	has_classic = "classic" in subprocess.check_output(
	["snap", "info", snap_name]
	).stdout.decode('utf-8')
	if has_classic:
	result = subprocess.run(
	["sudo", "snap", "install", snap_name, "--classic"]
	)
	else:
	result = subprocess.run(["sudo", "snap", "install", snap_name])
	if result.returncode != 0:
	print("Error adding snap: %s" % snap_name)
	exit(1)
	# add a sleep to give the snap a chance to finish
	subprocess.run(["sleep", "1"])


	def fix_snaps_or_exit(snaps: list) -> None:
	# check if we have root access
	if os.geteuid() != 0:
	print("Run this script as root to fix broken snaps")
	exit(1)
	# get the core snap
	core_snaps = [x for x in snaps if "canonical" in x]
	_fix_snaps_or_exit(core_snaps)
	# get the other snaps
	other_snaps = [x for x in snaps if "canonical" not in x]
	_fix_snaps_or_exit(other_snaps)


	# Fix the broken snaps
	fix_snaps_or_exit(broken_snaps)

	# if we still have broken snaps, we need to retry
	if len(get_broken_snaps_or_exit(BROKE_EXE)) > 0 and RETRY_COUNT > 1:
	print("Retrying to fix broken snaps")
	# run the script again
	subprocess.run(["./fixSnaps.py", BROKE_EXE, str(RETRY_COUNT - 1)])
	else:
	print("Failed to fix broken snaps")
	exit(1)
	#! /bin/bash

	#$1 is the executable that isn't working correctly

	# This script is used to modify the path priority for
	# the executable that is not working correctly

	# Store the output of `which` application for the executable
	execPaths=($(which -a $1))
	execPath="" # this will be the path that the user selects to prioritize

	# if the argument is not found, exit
	if [ $? -ne 0 ]; then
	echo "Error: $1 not found"
	exit 1
	fi
	# if there is only one path, then there are no alternatives, nothing to do
	if [ ${#execPaths[@]} -eq 1 ]; then
	echo "You have only one path to determine $1 ('${execPaths[0]}')"
	exit 1
	elif [ ${#execPaths[@]} -eq 2 ]; then
	echo -e "\e[0m\e[36mCurrently, '${execPaths[0]}' is the priority for $1."
	echo -e "Would you rather prioritize '${execPaths[1]}' instead (y/N)?\e[0m"
	read answer
	if [ "$answer" != "y" ]; then
	exit 1
	fi
	execPath=${execPaths[1]}
	else
	# tell the user what paths are determining the executable
	echo -e "\e[1;32mThe following paths determine which $1:"
	#loop through the paths
	for execPath in ${execPaths[@]}; do
	echo "$execPath"
	done
	PS3="Please enter the number of the path you would like to prioritize: "
	echo -e "\e[0m\e[36mWhich path do you want to \e[0m\e[36m\e[1mprioritize?\e[0m\e[36m"
	select execPath in ${execPaths[@]:1}; do
	# if the user selects a path, break out of the loop
	if [ $? -eq 0 ]; then
	break
	fi
	done
	fi

	# calculate unintended consequences
	affected=($(ls $execPath))
	bffected=( $(ls ${execPaths[0]}) )
	# calculate set intersection of `affected` and `bffected`
	common=($(comm -12 <(printf '%s\n' "${affected[@]}" \| LC_ALL=C sort) <(printf '%s\n' "${bffected[@]}" \| LC_ALL=C sort)))
	# warn about consequences
	echo -e "\e[31mWarning: Path re-ordering will also affect the following files:"
	for file in $common; do
	echo "$file"
	done

	echo -e "Do you want to continue? (y/N)\e[0m"
	read answer
	if [ "$answer" != "y" ]; then
	exit 1
	fi

	# reorder the system path to prioritize the selected path
	# first, remove the path from the system path
	PATH=$(echo $PATH \| sed -e "s;:$exePath;;")
	# then, add the path to the front of the system path
	PATH="$exePath:$PATH"

	# ask if the user wants to save the new path
	echo "Do you want to save the new path to your bash profile? (y/N)"
	read answer
	if [ "$answer" != "y" ]; then
	echo "Before export,"
	declareNewPath $1
	export PATH=$PATH
	echo "After export (which is not included in your bash profile),"
	declareNewPath $1
	exit 0
	fi

	# save the new path to the bash profile
	echo "export PATH=\"$PATH\"" >> ~/.bash_profile
	declareNewPath $1
	function declareNewPath() {
	# tell the user what the new path is that determines the executable
	echo "System declares that new path to $1 is:"
	echo "$( which $1 )"
	exit 0
	}