Brew upgrade get stuck in `removing...`

It’s still getting more or less stuck in that step:

Changing install name in /usr/local/Cellar/harfbuzz/2.5.1/lib/libharfbuzz.0.dylib
  from @@HOMEBREW_PREFIX@@/opt/graphite2/lib/libgraphite2.3.dylib
    to /usr/local/opt/graphite2/lib/libgraphite2.3.dylib
/usr/local/Homebrew/Library/Homebrew/postinstall.rb (Formulary::FromPathLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/harfbuzz.rb
🍺  /usr/local/Cellar/harfbuzz/2.5.1: 151 files, 10.0MB
Removing: /usr/local/Cellar/harfbuzz/2.5.0... (150 files, 10.0MB)
find /usr/local/Cellar/harfbuzz -name .DS_Store -delete
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/r.rb

I really don’t understand why it’s loading a formulae from core that aren’t installed in that step.

I tried to brew rm homebrew/core/r homebrew/core/cairo and it delete the ones from the other tap. I checked that no r or cairo formulae was installed and installed again the ones from the tap.

This is the tap of that formulae https://github.com/sethrfore/homebrew-r-srf

This is still happening almost every time I brew upgrade. Any idea? @srfore is the maintainer of the alternative tap for R and Cairo. Is this happening to you? Any idea what is going on here?

By the way… not it’s stuck in here and no R or Cairo related message.

Next week I’m going to change my computer and upgrade to Mojave, perhaps is something related with the last version Ruby and High Sierra?

At this point it’s probably worth adding more debugging information to your local installations of Homebrew and the formulae to figure out what’s going on.

Yes, this happens to me intermittently as well. I’ve no idea what is causing it and cannot systematically reproduce the problem. Moreover, I am running Mojave so it is unlikely OS related.

In terms of additional information, I currently have the Homebrew cask version of R installed for all personal related use as well as the Homebrew core versions of R and Cairo installed (not the versions maintained at https://github.com/sethrfore/homebrew-r-srf) due to external formula dependencies.

The only reason I’m using the cask R version rather than my own or the core version is due to a quartz graphics related issue where fonts and lines get blurred upon resizing the plotting device. I have no idea if others have had this issue or it in any way relates to the subject at hand.

In short, I don’t know if brew upgrade hangs due to an issue with my tap or multiple versions of R being installed or something else entirely.

Also, just so you all know, I am no expert in any of this so it certainly could relate to my tap. If there are problems or other ways it could be improved to integrate better with other Homebrew formulas, I’d be happy implement them to the extent my skill allows!

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Definitely smells R and/or Cairo related.

I’m seeing this too, and also only have the ‘standard’ versions of r and cairo installed because of dependencies. I’d be happy to help debug - how would you suggest “adding debugging information”?

Debugging information can be obtained by running the relevant command with --debug --verbose and pasting your brew config and brew doctor in here. What would be better still is to modify Homebrew’s source code to output things with puts or p or pp so you can get a sense of where exactly things are getting stuck.

It’s also worth asking: how long is it being left before it’s deemed to be stuck? 1 minute, 5 minutes, 1 hour, 5 hours?

Ah, that’s maybe getting us somewhere. Running upgrade just now with --debug --verbose shows it’s actually stuck on ==> Checking dependents for broken library links. The ruby process then takes up a lot of cpu - I’ve let it run for hours before.

Brew config:

HOMEBREW_VERSION: 2.1.6-18-g9a1936c
ORIGIN: https://github.com/Homebrew/brew
HEAD: 9a1936cd4b773dbd74695d3c110583570b58771b
Last commit: 5 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 489783c90329f48c3fd51a89b5ab715b4851b891
Core tap last commit: 5 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_NO_ANALYTICS_THIS_RUN: 1
CPU: quad-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1001
Git: 2.22.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 1.8.0_31
macOS: 10.14.5-x86_64
CLT: 10.2.1.0.1.1554506761
Xcode: 10.2.1
CLT headers: 10.2.1.0.1.1554506761
XQuartz: 2.7.11 => /opt/X11

Brew doctor:

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:
  openjpeg

Warning: Some installed formulae are missing dependencies.
You should `brew install` the missing dependencies:
  brew install postgresql proj

Run `brew missing` for more details.

The warnings are caused by having osgeo4mac’s qgis, which is stuck outside of homebrew because of this issue.

Actually, that just completed after about 25 minutes in total for one libssh upgrade. Hmm.

it’s stuck more than one minute for sure… and I’ve caught it stuck more than one hour there. In general when it’s there for a while —more than 10’— I usually ctrl-c it and that’s it.

How many packages do you all have installed (brew list | wc -l)? Do you have SSDs?

353 packages, yes to SSD.

356 packages and yes too to de SSD.

It’s now been stuck for 90 minutes after upgrading poppler.

@MikeMcQuaid you mentioned putsing a few things could help debugging - any suggestions for where we could place them?

@grischard I don’t have any specific locations in mind but you can start in cmd/upgrade.rb and “work down”.

I have been experiencing the same problem for some months now. I will try to contribute doing my own analysis (I hope to be able to) and take a place here to be updated on the issue.

I followed most of the advice in this thread, and it seemed to have fix the problem. It looked it was hanged but in reality it was solving some process. However, the last three days it has been hanging for hours at the following point:

==> Checking dependents for outdated formulae
==> No dependents to upgrade
==> Checking dependents for broken library links

I am not sure why this is happening. I hope someone may be able to help.

Just wanted to chime in and say that I update my system every morning, and a week or so ago I started having the problem described above: It hangs at:

Checking dependents for broken library links

and does so for five or six hours (it does eventually complete). It seems not to be related to what is being upgraded.

I do have HOMEBREW_INSTALL_CLEANUP=1 set, and I also install everything with the --build-from-source flag. I suppose I can unset routine cleanups and only do it once in awhile as an all-night process, but I suspect something is actually wrong here . . .

I also notice that whatever process is hanging is taking up a ton of memory and doesn’t seem to be niced down (very much). The system is hard to operate when it’s doing this.

Hey!

Do you have any of the offending libraries —R, Cairo, or anything form osgeo?