Rather fond of git and don't want to lose it. Is it safe to run brew link as suggested here:
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
git
Short answer: Yes, it is safe to do that.
Note also that OS X comes with git in /usr/bin, so you don't really need the brewed Git.
The warning message is mainly targeted at packages that provide libraries that other packages link against. That is not the case for git.
Related
Please help understand what is going on--or whether any action is required. I've gone through a lot of posts on dealing with brew, node, symlink, uninstalled and reinstalled node, npm, yarn, tried brew cleanup. When brew doctor produced these warnings--
Warning: Broken symlinks were found. Remove them with `brew prune`:
/usr/local/lib/node_modules/npm/node_modules/.bin/JSONStream
/usr/local/lib/node_modules/npm/node_modules/.bin/errno
/usr/local/lib/node_modules/npm/node_modules/.bin/is-ci
/usr/local/lib/node_modules/npm/node_modules/.bin/node-gyp
/usr/local/lib/node_modules/npm/node_modules/.bin/opener
/usr/local/lib/node_modules/npm/node_modules/.bin/qrcode-terminal
/usr/local/lib/node_modules/npm/node_modules/.bin/rc
/usr/local/lib/node_modules/npm/node_modules/.bin/semver
/usr/local/lib/node_modules/npm/node_modules/.bin/sshpk-conv
/usr/local/lib/node_modules/npm/node_modules/.bin/sshpk-sign
/usr/local/lib/node_modules/npm/node_modules/.bin/sshpk-verify
/usr/local/lib/node_modules/npm/node_modules/.bin/uuid
/usr/local/lib/node_modules/npm/node_modules/.bin/which
When I tried brew prune, I got:
newmbp$ brew link node
Warning: Already linked: /usr/local/Cellar/node/10.11.0
I noticed the files (to be linked or unlinked) are in separate folders, but have been struggling to understand the implications of having files in /usr/local/Cellar vs in /usr/local/lib
The precipitating factor that led to all of this was the fan on my laptop runs furiously from time to time, often while MAMP is running.
brew cleanup --prune-prefix (ex- brew prune) removed the broken symlinks, so the issue should be gone.
The fact that brew link node complains has nothing to do with this; it’s a completely different command. It’s not even an error, just a warning: "you asked me to link node but it’s already linked" so everything’s fine here.
Homebrew installs its files in /usr/local/Cellar. On the other hand, /usr/local/lib is a shared directory commonly used for libraries. In order for software to find libs Homebrew installed, it symlinks them in it.
For example, let’s say you have a formula foo version 1.2.3 that installs a library bar. After running brew install foo you should get something like this:
# the library files
/usr/local/Cellar/foo/1.2.3/lib/bar
# a symlink to the library files from /usr/local/lib
/usr/local/lib/bar -> /usr/local/Cellar/foo/1.2.3/lib/bar
If you brew uninstall foo, it removes both the library files and the symlink.
Those Homebrew symlinks can be manipulated with brew unlink <formula> (remove them) and brew link <formula> (add them). brew install runs brew link for you so you don’t need to. This is the reason why you get a warning: your Node symlinks already exist.
brew doctor performs various checks, including check_for_broken_symlinks. This one looks into directories such as /usr/local/var or /usr/local/lib for broken symlinks. A broken symlink is a symlink whose target doesn’t exist, often because it has been removed.
The important point to understand here is that Homebrew looks at all symlinks, not just the ones it created. Broken symlinks may cause issues, which is why Homebrew warns you about them, but if everything’s working fine for you feel free to ignore the warning.
After installing and uninstalling some programs through brew and brew cask, now I get brew doctor saying "unlinked kegs in your Cellar".
It suggests to link them, to avoid build trouble with later brews, but instead I'd rather delete them, as they're leftovers from brew programs or formulas that I don't use anymore.
How or where do I remove these? (I don't even know what a keg, or the Cellar, is)
Run:
brew remove packageName
for each unlinked package.
2018 Update
$ brew link --help
If --overwrite is passed, Homebrew will delete files which already exist
in the prefix while linking.
$ brew link --overwrite [package]
$ brew doctor
running brew link will bring up optional commands that you can use, along with that you'll need an argument to go with it or it'll prompt you with an error saying just that.
so I would suggest running:
brew doctor
This will give you the:
'Warning: You have unlinked kegs in your Cellar...'
message
underneath this message it will prompt which kegs are there with the potential problem.
My personal warning was:
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
mongodb
brew link
read your options, so you understand what is happening with this command.
brew link --dry-run <yourArgument>
Homebrew will list all files which would be linked or which would be deleted by brew link --overwrite, but will not actually link or delete any files.
brew link --overwrite <yourArgument>
This will execute what the dry-run did, for real this time.
My experience with this was:
cli cmnd:brew link --overwrite mongodb
cli response: Linking /usr/local/Cellar/mongodb/3.2.7... 0 symlinks created
brew doctor
Finally I ran this command and my response no longer had issues.
cli response: Your system is ready to brew.
I figure it will either make the link or if there is none to be had it will just delete the file; which was a previous solution above (this just seems to follow the brew cli prompts vs. just "smashing" the issue with a hammer).
I hope this helps you!
don't cry over spilt code, keep supporting the community.
After installing homebrew on Mac I had the following error:
$ 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 or file an issue; just ignore this. Thanks!
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
libtool
libksba
libyaml
libgpg-error
After running brew link libtool I would get the following error:
$ brew link libtool
Linking /usr/local/Cellar/libtool/2.4.6_1...
Error: Could not symlink include/libltdl
/usr/local/include is not writable.
But as it turned out I didn't have a folder /usr/local/include at all.
So I created it. And then changed the owner and group of the new folder to match the other folders in /usr/local. The next error was the same for /usr/local/lib, so I followed the same process.
After creating those two folders, brew link [package] worked.
brew 1.9.0
brew cleanup [options] [formula|cask]
Remove stale lock files and outdated downloads for all formulae and casks, and
remove old versions of installed formulae. If arguments are specified, only do
this for the given formulae and casks.
--prune Remove all cache files older than specified
days.
-n, --dry-run Show what would be removed, but do not
actually remove anything.
-s Scrub the cache, including downloads for
even the latest versions. Note downloads
for any installed formula or cask will
still not be deleted. If you want to delete
those too: rm -rf "$(brew --cache)"
--prune-prefix Only prune the symlinks and directories
from the prefix and remove no other files.
-v, --verbose Make some output more verbose.
-d, --debug Display any debugging information.
-h, --help Show this message.
Older versions
brew prune [--dry-run]:
Remove dead symlinks from the Homebrew prefix. This is generally not
needed, but can be useful when doing DIY installations. Also remove broken
app symlinks from /Applications and ~/Applications that were previously
created by brew linkapps.
If --dry-run or -n is passed, show what would be removed, but do not
actually remove anything.
rm /usr/local/Library/Taps/josegonzalez
-or if you are frightened-
mv /usr/local/Library/Taps/josegonzalez /usr/local/Library
Alike for other conflicting, but unlinked kegs/taps.
You can also use the provided info from the console and link them again:
Run `brew link`
Do this for each item listed, and everything should be fixed soon.
I ran brew doctor and got a few warning messages that I think I know what actions to take to fix, but want to see if I'm on the right track. Here is the list of warnings I received:
Warning: /usr/local/lib/pkgconfig 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/pkgconfig
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/mann
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/libtcl8.6.dylib
/usr/local/lib/libtk8.6.dylib
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.pc
Warning: Unbrewed static libraries 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 static libraries:
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
libyaml
For the first case, should I run chown <user>/usr/local/lib/pkgconfig
Warning: /usr/local/lib/pkgconfig 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/pkgconfig
Then chown <user>/usr/local/share/man/mann for the next message
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/mann
Not sure what to do for these warnings about deleting files. (???)
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/libtcl8.6.dylib
/usr/local/lib/libtk8.6.dylib
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.pc
Warning: Unbrewed static libraries 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 static libraries:
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
Finally run brew link libyaml?
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
libyaml
To fix the permissions problems, you can chown -R your_username /usr/local to recursively change ownership of everything under /usr/local.
You should brew link libyaml.
The warnings about dylibs tell you that you have a Tcl/Tk library installed to /usr/local. If you know how it got there and you know you do not need it, you can uninstall it. If you don't know how it got there, you can rename its files so builds won't pick it up (and so you can put them back if you discover that something depends on them). It's probably fine to leave it in place unless and until something breaks in a Tk-related way; it's possible it will never cause you trouble.
I solved the issue by running sudo chown <user>/usr/local/lib/pkgconfig, sudo chown <user>/usr/local/share/man/mann.
Then I deleted the files recommended and ran brew link libyaml and everything was fine.
After much searching on the Internet, I have never seen a satisfactory answer or explanation to the following problem. I would like to use CocoAspell for system-wide spell-checking on OS X 10.9 (plugs into TexShop, TextMate, etc.), but every time I install it, brew doctor starts throwing the following warnings:
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/libaspell.15.1.4.dylib
/usr/local/lib/libpspell.15.1.4.dylib
Warning: Unbrewed .la files 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 .la files:
/usr/local/lib/libaspell.la
/usr/local/lib/libpspell.la
Internet searches have shown that these warnings never seem to lead to any errors, but it seems to me that there must be some way to suppress them. Partly, I like to see the Your system is ready to brew notification, but I'd also like to avoid some sort of "boy crying wolf" situation, where I become accustomed to brew doctor throwing errors.
Is there a way to either:
Install CocoAspell in another location, such that brew doesn't see it
Hide the offending dylib and .la files from brew doctor
Or enable the CocoAspell preference pane/program to access libraries installed by a brewed version of aspell
Uninstalling CocoAspell and trashing the offending files results in a clean bill of health, and performing brew install aspell results in a working version of aspell, but this doesn't help me with any of the GUI applications I prefer for LaTeX editing.
Uninstall cocoAspell completely if you installed it before.
Install aspell with homebrew or any other package manager. Don't forget the dictionaries you need. I wanted English and Czech, so I used
brew install aspell --with-lang-cs --with-lang-en
Install only the preference pane of cocoAspell. Click on "Customize" before installing and only select the "Spelling" option.
Create the directory /Library/Application Support/cocoAspell/
Make a symlink in the directory to make the preference pane aware of the available dictionaries (as the administrator):
cd /Library/Application\ Support/cocoAspell/
ln -s /usr/local/lib/aspell-0.60 Dictionaries
Make sure that /usr/local/lib/aspell-0.60 is the correct path.
The cocoAspell pref pane now shows the installed dictionaries.
Add the offending files to the white_list in doctor.rb. Mine was in /usr/local/Library/Homebrew/cmd/doctor.rb
If your's isn't there, find it with
locate doctor.rb
Look for white_list in side of def check_for_stray_dylibs, mine was on line 105. It should probably look like this.
white_list = {
"libfuse.2.dylib" => "MacFuse",
"libfuse_ino64.2.dylib" => "MacFuse",
"/usr/local/lib/libTrAPI.dylib" => "TrAPI"
}
An alternative is to install Homebrew somewhere other than /usr/local (that is, create ~/.homebrew, or /Tools/homebrew; then sudo chmod $USER /Tools/homebrew, untar Homebrew there, and add /Tools/homebrew/bin to your $PATH). That way, /usr/local is reserved for things you're installed there by some other means, rather than using Homebrew; for example the situation you describe here. Homebrew still occasionally whines about it, but you can usually ignore it.
I use Homebrew as my principal OS X package manager; I don't let it anywhere near /usr/local.
Note that this advice is the direct opposite of Homebrew's insistent dogma, which I myself find unpersuasive.
I'm very much a newbie when it comes to all this so forgive my incompetence.
When I run brew Doctor, I get the following. Can someone help?
[/usr/local]$ brew doctor
Error: Setting DYLD_LIBRARY_PATH can break dynamic linking.
You should probably unset it.
Error: Some keg-only formula are linked into the Cellar.
Linking a keg-only formula, such as gettext, into the cellar with
brew link f will cause other formulae to detect them during the
./configure step. This may cause problems when compiling those
other formulae.
Binaries provided by keg-only formulae may override system binaries
with other strange results.
You may wish to brew unlink these brews:
libxml2
Error: 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/libcharset.1.dylib /usr/local/lib/libfreetype.6.dylib /usr/local/lib/libjpeg.8.dylib /usr/local/lib/liblcms.1.0.19.dylib /usr/local/lib/libMagickCore.4.dylib /usr/local/lib/libMagickWand.4.dylib /usr/local/lib/libpng15.15.dylib /usr/local/lib/libtiff.3.dylib /usr/local/lib/libtiffxx.3.dylib /usr/local/lib/libwmf-0.2.7.1.0.dylib /usr/local/lib/libwmflite-0.2.7.0.1.dylib
Error: Unbrewed .la files 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 .la files:
/usr/local/lib/libcharset.la /usr/local/lib/libfreetype.la /usr/local/lib/libjpeg.la /usr/local/lib/liblcms.la /usr/local/lib/libMagickCore.la /usr/local/lib/libMagickWand.la /usr/local/lib/libpng15.la /usr/local/lib/libtiff.la /usr/local/lib/libtiffxx.la /usr/local/lib/libwmf.la /usr/local/lib/libwmflite.la
Error: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/freetype2.pc /usr/local/lib/pkgconfig/ImageMagick.pc /usr/local/lib/pkgconfig/lcms.pc /usr/local/lib/pkgconfig/libpng15.pc /usr/local/lib/pkgconfig/MagickCore.pc /usr/local/lib/pkgconfig/MagickWand.pc /usr/local/lib/pkgconfig/Wand.pc
Error: Unbrewed static libraries 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 static libraries:
/usr/local/lib/libcharset.a /usr/local/lib/libfreetype.a /usr/local/lib/libjpeg.a /usr/local/lib/liblcms.a /usr/local/lib/libpng15.a /usr/local/lib/libtiff.a /usr/local/lib/libtiffxx.a /usr/local/lib/libwmf.a /usr/local/lib/libwmflite.a
Error: You have uncommitted modifications to Homebrew's core.
Unless you know what you are doing, you should run:
cd /usr/local && git reset --hard
Error: Some directories in your path end in a slash.
Directories in your path should not end in a slash. This can break other
doctor checks. The following directories should be edited:
/usr/local/git/bin/
[/usr/local]$
Error: Setting DYLD_LIBRARY_PATH can break dynamic linking. You should probably unset it. Error: Some keg-only formula are linked into the Cellar. Linking a keg-only formula, such as gettext, into the cellar with brew link f will cause other formulae to detect them during the ./configure step. This may cause problems when compiling those other formulae.
Binaries provided by keg-only formulae may override system binaries with other strange results.
This is asking you to unset your Dynamic Loading Library Path. You can do this by finding out where you set it and removing it. Most likely, you have a line in your ~/.bashrc or ~/.bash_profile that looks like export DYLD_LIBRARY_PATH=/some/path:$DYLD_LIBRARY_PATH
You may wish to brew unlink these brews:
libxml2
When Brew links, it's creating a symlink to the installation. It's how you can have python2.6. python2.7 installed but python will run one of them.
brew unlink libxml2
Error: 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/libcharset.1.dylib /usr/local/lib/libfreetype.6.dylib /usr/local/lib/libjpeg.8.dylib /usr/local/lib/liblcms.1.0.19.dylib /usr/local/lib/libMagickCore.4.dylib /usr/local/lib/libMagickWand.4.dylib /usr/local/lib/libpng15.15.dylib /usr/local/lib/libtiff.3.dylib /usr/local/lib/libtiffxx.3.dylib /usr/local/lib/libwmf-0.2.7.1.0.dylib /usr/local/lib/libwmflite-0.2.7.0.1.dylib Error: Unbrewed .la files 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 .la files: /usr/local/lib/libcharset.la /usr/local/lib/libfreetype.la /usr/local/lib/libjpeg.la /usr/local/lib/liblcms.la /usr/local/lib/libMagickCore.la /usr/local/lib/libMagickWand.la /usr/local/lib/libpng15.la /usr/local/lib/libtiff.la /usr/local/lib/libtiffxx.la /usr/local/lib/libwmf.la /usr/local/lib/libwmflite.la Error: Unbrewed .pc files were found in /usr/local/lib/pkgconfig. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.
Unexpected .pc files: /usr/local/lib/pkgconfig/freetype2.pc /usr/local/lib/pkgconfig/ImageMagick.pc /usr/local/lib/pkgconfig/lcms.pc /usr/local/lib/pkgconfig/libpng15.pc /usr/local/lib/pkgconfig/MagickCore.pc /usr/local/lib/pkgconfig/MagickWand.pc /usr/local/lib/pkgconfig/Wand.pc Error: Unbrewed static libraries 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 static libraries: /usr/local/lib/libcharset.a /usr/local/lib/libfreetype.a /usr/local/lib/libjpeg.a /usr/local/lib/liblcms.a /usr/local/lib/libpng15.a /usr/local/lib/libtiff.a /usr/local/lib/libtiffxx.a /usr/local/lib/libwmf.a /usr/local/lib/libwmflite.a
These are residual files from other installations. You can delete them.
rm FILENAME
Error: You have uncommitted modifications to Homebrew's core. Unless you know what you are doing, you should run: cd /usr/local && git reset --hard
Here, it is telling you that you made modifications to Homebrew files. Luckily, Homebrew is stored in Git version control so you can revert those changes.
cd /usr/local && git reset --hard
Error: Some directories in your path end in a slash. Directories in your path should not end in a slash. This can break other doctor checks. The following directories should be edited: /usr/local/git/bin/
The PATH variable is where your computer searches for programs when you type it in the command line. You can see your path with echo $PATH.
Standards dictate that all the paths in PATH should not end in a slash. Thus, homebrew is asking you to fix it.
nano ~/.bashrc or nano ~/.bash_profile and look for '/usr/local/git/bin/' and remove the trailing slash.
I'm new to brew as well. When I first tried, I ended up with a laundry list of errors. Not all needed to be fixed for me to use brew as I needed it. In particular, I was able to ignore the
Unbrewed * were found in /usr/local/lib
messages that I was getting. I believe those are only a problem when your use of brew installed packages will interfere with ones you've installed before (in my case, it was NTFS-3g, not related to my future uses of brew).