`brew cleanup` has not been run in 30 days, running now... at every brew upgrade


(Jendker) #1

Hello everyone,

Since the update to brew 2.0.0 and introduction of automatic cleanup the cleanup is executed for me every single time I am doing brew upgrade. This wouldn’t be all that tragic, the problem is that brew cleanup is executed after the upgrade of each keg stopping the upgrade process, so that I need to rerun brew upgrade to upgrade next keg and so on until all are upgraded.

Currently I am on brew 2.0.1 and the problem still persists:

$ brew --version
Homebrew 2.0.1
Homebrew/homebrew-core (git revision 2b164; last commit 2019-02-09)

I didn’t find any such issue online. What can be the cause and how to deal with it? Brew doctor is clean, just shows some broken symlinks of ghostscript caused by installed MacTeX.


(Alex Semyonov) #2

Have almost the same “brew cleanup has not been run in 30 days, running now…” everyday (or even more often).


(Jendker) #3

For completeness, here is brew config output:

HOMEBREW_VERSION: 2.0.1
ORIGIN: https://github.com/Homebrew/brew
HEAD: e32c1515432a938093d5ef1d8c4b4408991873df
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 2b1646311ab3f9fa9644b6ee657dc4240bfacb37
Core tap last commit: 23 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_LOGS: /Users/Jedrzej/Library/Logs/Homebrew
CPU: octa-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.2 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
macOS: 10.14.3-x86_64
CLT: N/A
Xcode: 10.1

And 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: Broken symlinks were found. Remove them with `brew cleanup`:
  /usr/local/share/ghostscript/9.23/Resource/CIDFSubst/ipaexg.ttf
  /usr/local/share/ghostscript/9.23/Resource/CIDFSubst/ipaexm.ttf
  /usr/local/share/ghostscript/9.23/Resource/CIDFSubst/ipag.ttf
  /usr/local/share/ghostscript/9.23/Resource/CIDFSubst/ipam.ttf
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  /usr/local/share/ghostscript/9.23/Resource/Font/blex.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/blsy.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/cmb10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/cmbsy10.pfb
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  /usr/local/share/ghostscript/9.23/Resource/Font/cmbsy8.pfb
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  /usr/local/share/ghostscript/9.23/Resource/Font/cmbx10.pfb
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  /usr/local/share/ghostscript/9.23/Resource/Font/cmbx5.pfb
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  /usr/local/share/ghostscript/9.23/Resource/Font/cmbx9.pfb
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  /usr/local/share/ghostscript/9.23/Resource/Font/msbm7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/msbm8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/msbm9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omding.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea1.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea1b.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea2.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea2b.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea3.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsea3b.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omseco.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecob.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecobi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecoi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecx.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecy.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecyb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsecyi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsegr.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsegrb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsegrbi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsegri.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omseha.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsehe.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omseip.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omsela.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omselab.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omselabi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omselai.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omseti.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/omssti.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plb10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbsy10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx6.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbx9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbxsl10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plbxti10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plcsc10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pldunh10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plex10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plex9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plff10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plfi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plfib8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plinch.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plitt10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi6.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmi9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plmib10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr6.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plr9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsl10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsl12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsl8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsl9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsltt10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plss10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plss12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plss17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plss8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plss9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssbi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssbx10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssdc10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssi12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssi17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssi8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssi9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssq8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plssqi8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy6.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plsy9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltcsc10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltex10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltex8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltex9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plti10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plti12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plti7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plti8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plti9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltt10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltt12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltt8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pltt9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plu10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/plvtt10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/putb8a.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/putbi8a.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/putr8a.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/putri8a.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbex.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbexa.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbmia.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbsy.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbsya.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbsyb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxbsyc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxex.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxexa.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxmia.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxsy.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxsya.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxsyb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/pxsyc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rblmi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpcxb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpcxbi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpcxi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpcxr.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxbi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxbmi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxbsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxmi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxr.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rpxsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rsfs10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rsfs5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rsfs7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxbi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxbss.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxr.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtcxss.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxb.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxbi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxbmi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxbsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxbss.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxbsssc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxmi.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxr.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxss.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/rtxsssc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary5.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary6.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary7.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/stmary9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/t1xbtt.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/t1xbttsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/t1xtt.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/t1xttsc.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tcxbtt.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tcxtt.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipa10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipa12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipa17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipa8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipa9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipab10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipabs10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipabx10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipabx12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipabx8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipabx9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasb10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasl10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasl12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasl8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipasl9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipass10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipass12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipass17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipass8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipass9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipats10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipatt10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipatt12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipatt8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipatt9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipx10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipx12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipx17.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipx8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipx9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxb10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxbs10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxbx10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxbx12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxbx8.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxbx9.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxsb10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxsi10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxsl10.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxsl12.pfb
  /usr/local/share/ghostscript/9.23/Resource/Font/tipxsl8.pfb
  ... more ghostscript output ...

(Jonathan Chang) #4

Are you letting the cleanup command run to completion or are you canceling it after the formula you want is upgraded? brew cleanup can take a long time if you’ve never run it before. Try running just brew cleanup once (without arguments) and see if that speeds up subsequent runs.

Alternatively, if you’re running brew in an unusual setup (e.g., off of a network share) it might also slow things down. Finally, very slow cleanup might also be a sign of impending disk failure, since it does a lot of I/O and disk errors would slow it down even more.


(Jendker) #5

I was running brew cleanup manually prior to version 2.0.0, so for sure it was less than 30 days since last brew cleanup, but it is still automatically erformed.

Answering to your question: I am always letting brew cleanup finish after brew update and then I need to start the next brew update, because only one keg is being updated as described in the first post. After it brew cleanup is going to be automatically executed again. And it goes on until I update all the kegs one by one. I hope it is clear how it all happens.


(Jendker) #6

Ok, I have an idea what may be the problem, thanks for asking @jonchang if I let the process finish.

I let the process finish, but at the end of brew update I get:

Error: Permission denied @ unlink_internal - /usr/local/share/ghostscript/9.23/Resource/CIDFSubst/ipaexg.ttf

Maybe that’s why it doesn’t mark brew update as finished?
What can I do about this error? Should I run brew cleanup as root? This is due to the installed MacTeX http://www.tug.org/mactex/, which causes also the brew doctor warning, which I posted in the output in previous post.


(Jonathan Chang) #7

Yeah installing mactex would cause this issue. I’d recommend installing mactex via homebrew cask instead, which properly handles the interaction between Tex and homebrew. In particular, it’ll install mactex without the bundled Ghostscript and use homebrew’s ghostscript instead, eliminating this issue.


(Gideon Simpson) #8

I have the exact same issue. At some point I uninstalled MacTex (and have since gone to rely on MacPorts TeXLive, but that’s another issue). What’s the “safe” way to remove these files for home-brew? I saw some suggestion about changing all the permissions, but that sounds like a terrible idea.


(Jendker) #9

I don’t know if that answers your question, but I removed MacTeX according to this link https://www.tug.org/mactex/uninstalling.html and after it I just had to change permission to /usr/local/share/doc/ghostscript. I guess I omitted this folder in the uninstall process.

At the end I installed MacTeX with brew cask and I could luckily finish brew cleanup without any errors.

EDIT: And this have also solved my problem with brew cleanup being executed on every brew upgrade. I just had to resolve the error which was breaking the cleanup process.