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brew doctor errors #39964

Closed ccorcos closed 9 years ago

ccorcos commented 9 years ago

it says to chown /usr/local/include. What permission flags should I use? I can't brew update either due to these permissions

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: /usr/local/include isn't writable.

This can happen if you "sudo make install" software that isn't managed by
by Homebrew. If a formula tries to write a file to this directory, the
install will fail during the link step.

You should probably `chown` /usr/local/include

Warning: /usr/local/lib isn't writable.

This can happen if you "sudo make install" software that isn't managed by
by Homebrew. If a formula tries to write a file to this directory, the
install will fail during the link step.

You should probably `chown` /usr/local/lib

Warning: /usr/local/share isn't writable.

This can happen if you "sudo make install" software that isn't managed by
by Homebrew. If a formula tries to write a file to this directory, the
install will fail during the link step.

You should probably `chown` /usr/local/share

Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:

    /usr/local/share/man
    /usr/local/share/man/man1

Warning: The /usr/local directory is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. Some versions of the
"InstantOn" component of Airfoil are known to do this.

You should probably change the ownership and permissions of /usr/local
back to your user account.

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libwkhtmltox.0.12.2.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
    /usr/local/include/wkhtmltox/image.h
    /usr/local/include/wkhtmltox/pdf.h

Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.
DomT4 commented 9 years ago

sudo chown -Rwhoami/usr/local will do the trick.

ccorcos commented 9 years ago

Ok. That worked for chown stuff. I removed the unexpected header files and did brew prune.

Then I ran brew doctor and got this

~ ❯❯❯ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: The /usr/local directory is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. Some versions of the
"InstantOn" component of Airfoil are known to do this.

You should probably change the ownership and permissions of /usr/local
back to your user account.

Not sure what to do about that... Then I tried brew update and got the following

~ ❯❯❯ brew update                                                                                                                                    
error: unable to unlink old 'CODEOFCONDUCT.md' (Permission denied)
error: unable to unlink old 'SUPPORTERS.md' (Permission denied)
Error: Failure while executing: git pull -q origin refs/heads/master:refs/remotes/origin/master
~ ❯❯❯ brew doctor                                                                                                                                    
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: The /usr/local directory is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. Some versions of the
"InstantOn" component of Airfoil are known to do this.

You should probably change the ownership and permissions of /usr/local
back to your user account.

Warning: You have uncommitted modifications to Homebrew
If this a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
    cd /usr/local/Library && git stash && git clean -d -f

Warning: Your Xcode (6.3.1) is outdated
Please update to Xcode 6.3.2.
Xcode can be updated from the App Store.
DomT4 commented 9 years ago

Warning: The /usr/local directory is not writable. Even if this directory was writable when you installed Homebrew, other software may change permissions on this directory. Some versions of the "InstantOn" component of Airfoil are known to do this.

Hmm. Can you do ls -l /usr and paste the output?

You can also see what modifications it's complaining about by doing cd /usr/local && git status.

ccorcos commented 9 years ago 
~ ❯❯❯ ls -l /usr                                                                                                                                      ⏎
total 16
drwxr-xr-x     5 root  wheel    170 Sep  9  2014 X11
lrwxr-xr-x     1 root  wheel      3 Oct 16  2014 X11R6 -> X11
drwxr-xr-x  1078 root  wheel  36652 Apr 28 12:21 bin
drwxr-xr-x   257 root  wheel   8738 May 21 12:42 include
drwxr-xr-x   271 root  wheel   9214 May 21 12:42 lib
drwxr-xr-x   171 root  wheel   5814 May  7 18:01 libexec
drwxr-xr-x    22 root  wheel    748 Jan 19 16:40 local
drwxr-xr-x   244 root  wheel   8296 Apr 28 12:21 sbin
drwxr-xr-x    44 root  wheel   1496 Oct 16  2014 share
drwxr-xr-x     4 root  wheel    136 Oct 16  2014 standalone
lrwxr-xr-x     1 root  wheel     44 Oct 16  2014 texbin -> ../Library/TeX/Distributions/Programs/texbin
~ ❯❯❯ cd /usr/local && git status
On branch master
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

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    modified:   Library/Homebrew/test/test_bottle_versions.rb
    modified:   Library/Homebrew/test/test_cmd_cleanup.rb
    modified:   Library/Homebrew/test/test_formula.rb
    deleted:    Library/Homebrew/test/test_formula_install.rb
    modified:   Library/Homebrew/test/test_hardware.rb
    modified:   Library/Homebrew/test/test_keg.rb
    modified:   Library/Homebrew/test/test_language_module_dependency.rb
    modified:   Library/Homebrew/test/test_pathname.rb
    modified:   Library/Homebrew/test/test_pkg_version.rb
    modified:   Library/Homebrew/test/test_versions.rb
    modified:   Library/Homebrew/test/testball.rb
    modified:   Library/Homebrew/test/testing_env.rb
    modified:   Library/Homebrew/utils.rb
    modified:   Library/Homebrew/version.rb
    modified:   Library/brew.rb
    modified:   share/doc/homebrew/Acceptable-Formulae.md
    modified:   share/doc/homebrew/FAQ.md
    modified:   share/doc/homebrew/Formula-Cookbook.md
    modified:   share/doc/homebrew/Gems,-Eggs-and-Perl-Modules.md
    modified:   share/doc/homebrew/How-To-Open-a-Homebrew-Pull-Request-(and-get-it-merged).md
    modified:   share/doc/homebrew/Tips-N'-Tricks.md
    modified:   share/doc/homebrew/Xcode.md
    modified:   share/man/man1/brew.1

Untracked files:
  (use "git add <file>..." to include in what will be committed)

    Library/Aliases/awsebcli
    Library/Aliases/blazegraph
    Library/Aliases/kotlin
    Library/Aliases/pcre1
    Library/Aliases/speedtest-cli
    Library/Aliases/yubico-pam
    Library/ENV/4.3/g++-5
    Library/ENV/4.3/gcc-5
    Library/ENV/include/
    Library/Formula/apache-drill.rb
    Library/Formula/apel.rb
    Library/Formula/blockhash.rb
    Library/Formula/ccat.rb
    Library/Formula/cidrmerge.rb
    Library/Formula/clang-omp.rb
    Library/Formula/cppformat.rb
    Library/Formula/creduce.rb
    Library/Formula/cryptol.rb
    Library/Formula/curlpp.rb
    Library/Formula/cvc4.rb
    Library/Formula/dcd.rb
    Library/Formula/delta.rb
    Library/Formula/docker-machine.rb
    Library/Formula/efl.rb
    Library/Formula/elementary.rb
    Library/Formula/embulk.rb
    Library/Formula/envchain.rb
    Library/Formula/evas-generic-loaders.rb
    Library/Formula/exact-image.rb
    Library/Formula/ffms2.rb
    Library/Formula/flyway.rb
    Library/Formula/fpp.rb
    Library/Formula/fsevent_watch.rb
    Library/Formula/gdrive.rb
    Library/Formula/get-flash-videos.rb
    Library/Formula/git-hooks.rb
    Library/Formula/git-lfs.rb
    Library/Formula/git-octopus.rb
    Library/Formula/git-stree.rb
    Library/Formula/git-subrepo.rb
    Library/Formula/git-test.rb
    Library/Formula/gst-python.rb
    Library/Formula/gst-validate.rb
    Library/Formula/hebcal.rb
    Library/Formula/highlighting-kate.rb
    Library/Formula/http-parser.rb
    Library/Formula/jlog.rb
    Library/Formula/jpeg-archive.rb
    Library/Formula/jpegrescan.rb
    Library/Formula/jvgrep.rb
    Library/Formula/kafkacat.rb
    Library/Formula/karn.rb
    Library/Formula/kotlin-compiler.rb
    Library/Formula/libcdr.rb
    Library/Formula/libdbi.rb
    Library/Formula/libghthash.rb
    Library/Formula/librdkafka.rb
    Library/Formula/mergepbx.rb
    Library/Formula/moe.rb
    Library/Formula/mypy.rb
    Library/Formula/natalie.rb
    Library/Formula/nfdump.rb
    Library/Formula/ooniprobe.rb
    Library/Formula/pacapt.rb
    Library/Formula/packer.rb
    Library/Formula/pjproject.rb
    Library/Formula/pkcrack.rb
    Library/Formula/pkgdiff.rb
    Library/Formula/ponyc.rb
    Library/Formula/prettyping.rb
    Library/Formula/rapidjson.rb
    Library/Formula/remarshal.rb
    Library/Formula/rexster.rb
    Library/Formula/rofs-filtered.rb
    Library/Formula/scalariform.rb
    Library/Formula/sfk.rb
    Library/Formula/shpotify.rb
    Library/Formula/srclib.rb
    Library/Formula/sslyze.rb
    Library/Formula/swiftlint.rb
    Library/Formula/tasksh.rb
    Library/Formula/texmath.rb
    Library/Formula/thefuck.rb
    Library/Formula/tidy-html5.rb
    Library/Formula/trr.rb
    Library/Formula/validns.rb
    Library/Formula/watch-sim.rb
    Library/Formula/xonsh.rb
    Library/Formula/xsp.rb
    Library/Homebrew/config.rb
    Library/Homebrew/postinstall.rb
    Library/Homebrew/requirements/emacs_requirement.rb
    Library/Homebrew/requirements/ruby_requirement.rb
    Library/Homebrew/sandbox.rb
    Library/Homebrew/test.rb
    Library/Homebrew/test/fixtures/test.diff
    Library/Homebrew/test/lib/
    Library/Homebrew/test/test_formula_installer.rb
    Library/Homebrew/test/test_sandbox.rb
    Library/Homebrew/utils/fork.rb

no changes added to commit (use "git add" and/or "git commit -a")

Thanks for the help

DomT4 commented 9 years ago

drwxr-xr-x 22 root wheel 748 Jan 19 16:40 local

Try sudo chownwhoami/usr/local for this. That should fix the problem for the directory itself. I think the previously used -R option only works for directories inside the directory and not the top-level directory itself.

As for the git status reply, yikes :smile_cat:. Once you've fixed the top-level permissions just run git fetch; git reset --hard origin/master inside /usr/local.

ccorcos commented 9 years ago

Good to go :)

~ ❯❯❯ brew doctor
Your system is ready to brew.
~ ❯❯❯ brew update
Already up-to-date.

Thanks @DomT4 !

DomT4 commented 9 years ago

Awesome! :tada:. Happy to help!