Could you try to untap that tap or uninstall those formulae?
Hardly no… because I need it. But I think I have a theory about what could be the issue at least in origin.
I have some other formulae that depends in
R and therefore
Cairo, but the Core ones instead of the ones from this tap. Since I don’t want to uninstall and install when the dependents are updated, I just unlink those cellars —
cairo— and rename them. Brew installs the ones from core and after the install finish I just unlink the ones form core, delete them and the ones from the alternative tap and renamed back.
I’ll do a proper uninstall and install and let’s see how it turns out.
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
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!
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
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.
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 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.