Brew: Repeated `xorgproto`-related warnings output from several core commands (e.g. `doctor`, `leaves`)

[jaredsampson]

Please note that we will close your issue without comment if you delete, do not read or do not fill out the issue checklist below and provide ALL the requested information. If you repeatedly fail to use the issue template, we will block you from ever submitting issues to Homebrew again.

• [x] ran a brew command and reproduced the problem with multiple formulae? If it's a problem with a single, official formula (not cask) please file this issue at Linuxbrew/homebrew-core: https://github.com/Linuxbrew/homebrew-core/issues/new/choose. If it's a brew cask problem please file this issue at https://github.com/Homebrew/homebrew-cask/issues/new/choose. If it's a tap (e.g. Homebrew/homebrew-php) problem please file this issue at the tap.
• [x] ran brew update and can still reproduce the problem?
• [x] ran brew doctor, fixed all issues and can still reproduce the problem?

Fixed all issues I can--I'm on a shared system where I'm not an admin, so there are still extra .la/.pc/.a files in /usr/local/lib that I can't remove. I also have a conda installation that has several *-config scripts. Full brew doctor uploaded (see below).

• [x] ran brew config and brew doctor and included their output with your issue?

Both uploaded to: https://gist.github.com/jaredsampson/1339f500413970a047f0cf4736961bfa

What you were trying to do (and why)

Run brew doctor or missing, or leaves to check the status of my Linuxbrew installation, or brew uninstall XXX to uninstall a given formula.

What happened (include command output)

The commands run successfully, but also output every time a long list of warnings related to xorgproto and older, deprecated proto programs.

Command output

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated xproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated kbproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated renderproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated xextproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated bigreqsproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated compositeproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated damageproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated dmxproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated dri2proto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated dri3proto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated fixesproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated fontsproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated glproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated inputproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated kbproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated presentproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated randrproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated recordproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated renderproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated resourceproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated scrnsaverproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated videoproto

Warning: Use linuxbrew/xorg/xorgproto instead of deprecated xcmiscproto

...and this goes on for 250 lines

  

A complete version of the warnings is included in the same gist.

I find this unusual, particularly because I have xorgproto installed, but none of the deprecated programs:

$ brew list | grep proto
protobuf
xcb-proto
xorgproto

What you expected to happen

I would expect these warnings to tell me which formula specifies the deprecated programs, or to have some other way of finding out how to resolve the apparent dependency issue. It would be nice not to have 250 lines of warnings every time I run one of these basic commands, but I'm not sure how to go about fixing it.

Step-by-step reproduction instructions (by running brew commands)

For me, this happens every time I run one of the aforementioned commands (brew doctor, brew leaves, brew missing, brew uninstall X), with no other steps necessary. I suspect this will not be the case for other users or it would have been reported previously.

[sjackman]

@maxim-belkin Any thoughts on the cause of this issue?

[maxim-belkin]

@jaredsampson Could you please post (as a gist) the output of brew list?

[maxim-belkin]

Actually, could you please post (as a gist) the output you get upon executing these commands:

export HOMEBREW_DEBUG=1
brew doctor

[JuPlutonic]

Have these warnings "Warning: Use linuxbrew/xorg/xorgproto instead of deprecated".
((((I think something wrong with /home/l-b/.l-b/Library/Taps/linuxbrew/homebrew-xorg. I'm thinking about re-pour all bottles what actually comes from linuxbew/xorg.)))
I can reproduce warnings with Taps related formulas:
https://gist.github.com/JuPlutonic/f6a7ab40165b92e26f02a1c6a40182d7

PS: Sorry for my English.

[JuPlutonic]

See: homebrew-xorg/Formula/font-util.rb output3.log

export HOMEBREW_DEBUG=1
brew doctor

[jaredsampson]

I've added the brew list output to the previous gist I used before.

I'm in the middle of a brew upgrade which I had hoped might take care of this issue, so I'll wait until that's done to post the new brew doctor output with debug info, hopefully later today (I had quite a few things outdated, including some built from source).

[maxim-belkin]

@JuPlutonic, thanks for for log file. So, it is check_missing_deps that causes these warnings. I'll have a look into it.

Another question: why do you have

/home/linuxbrew/.linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/

and not

/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula

?

Have you tried

brew update
brew update
brew upgrade
brew cleanup --prune=0
brew prune

?

[maxim-belkin]

Thanks, @jaredsampson. Your problem might come from any of the outdated linuxbrew/xorg packages. The first thing I'd try is brew remove linuxbrew/xorg/xorg :)

[JuPlutonic]

Yep, did today many times (brew cleanup / brew update && brew update / brew cleanup --prune=0 && brew prune, brew upgrade I didn't use because I don't want pg to be upgraded)

[JuPlutonic]

Another question: why do you have

/home/linuxbrew/.linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/

and not

/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula

Yes

[maxim-belkin]

Yes

Thank you

[maxim-belkin]

Yep, did today many times (brew cleanup / brew update && brew update / brew cleanup --prune=0 && brew prune, brew upgrade I didn't use because I don't want pg to be upgraded)

Try this:

brew upgrade $(brew list | grep -v pg)

[sjackman]

Another question: why do you have /home/linuxbrew/.linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/ and not /home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula

Older installations of Linuxbrew used $REPOSITORY == $PREFIX, and those older installations are not automatically migrated automatically to the current directory structure of $REPOSITORY == $PREFIX/Homebrew.

[iMichka]

I found a similar problem on an older install where I ran an update right now.
I was able to debug this a little bit. brew doctor was for example triggering these warnings.

I put a raise just here: https://github.com/Linuxbrew/brew/blob/master/Library/Homebrew/formulary.rb#L248

It got stuck on libxcb and libx11. Uninstalling both and then rebuilding them from source fixed the problem for me. I guess that both bottles need to be rebuilt.

[sjackman]

Perhaps a patch to Homebrew/brew is warranted?

[jaredsampson]

@maxim-belkin My brew upgrade finished overnight last night, so I've posted the brew doctor output with debug info here.

Thanks for the debugging work, @iMichka. I'll try uninstalling those and reinstall from source as you suggest.

[jaredsampson]

@sjackman Looking at the code where @iMichka added the raise statement, it would help in narrowing down the source of these warnings by simply adding the name of the formula that has that particular dependency, perhaps something like:

opoo "#{name}: Use #{new_name} instead of deprecated #{old_name}"

although I just tried that, and it produces the errors:

Warning: xorgproto: Use linuxbrew/xorg/xorgproto instead of deprecated dri3proto

so being unfamiliar with the source, it seems must have the wrong variable.

[sjackman]

@jaredsampson That looks right to me. Try…

opoo "#{path}: Use #{new_name} instead of deprecated #{old_name}"

[maxim-belkin]

Looks like these lines are triggered:
https://github.com/Linuxbrew/brew/blob/aed454897a835834a62ced40609b66d876a99904/Library/Homebrew/formulary.rb#L230-L235
so, taking https://github.com/Linuxbrew/brew/issues/909#issuecomment-451746038 as an example, name = dri3proto...
We have to figure out where that dri3proto comes from given that it is not installed (according to brew list).

[JuPlutonic]

Any changes in L248 didn't give me any clue(yhe raised error/ more complex message shows that xorgproto found problem in itself… maybe linuxbrew/xorg/xorgproto != xorgproto).
I think what on L227/L230 we need some more checks.

[maxim-belkin]

What does it say when you change line 248 to

opoo "#{path}: Use #{new_name} instead of deprecated #{old_name}"

?

[JuPlutonic]

@maxim-belkin
output2.txt
…
Warning: /opt/.linuxbrew/Homebrew/Library/Taps/linuxbrew/homebrew-xorg/Formula/xorgproto.rb: Use linuxbrew/xorg/xorgproto instead of deprecated xorg-protocols
…
I did
export HOMEBREW_DEBUG=1; brew remove --debug font-inconsolata-nerd-font
from tap ta2gch/fonts

[jaredsampson]

@sjackman using path instead of name in L248 I get:

Warning: /home/ME/.linuxbrew/Homebrew/Library/Taps/linuxbrew/homebrew-xorg/Formula/xorgproto.rb: Use linuxbrew/xorg/xorgproto instead of deprecated dri3proto

And yes, as @maxim-belkin noted, dri3proto is not installed. I actually tried installing it and got this:

$ brew install dri3proto
Updating Homebrew...
Warning: linuxbrew/xorg/xorgproto 2018.4 is already installed and up-to-date
To reinstall 2018.4, run `brew reinstall xorgproto`

So apparently dri3proto (and presumably others) somehow alias to xorgproto?

I see a couple pull requests, but no formula for it.

$ brew search dri3proto
No formula or cask found for "dri3proto".
Closed pull requests:
new formulae: dri3proto (https://github.com/Homebrew/homebrew-core/pull/11843)
openni2 2.2.0-debian (https://github.com/Homebrew/homebrew-science/pull/5192)

[sjackman]

Just to be sure, dri3proto is not reference in that file?

grep dri3proto /home/ME/.linuxbrew/Homebrew/Library/Taps/linuxbrew/homebrew-xorg/Formula/xorgproto.rb
echo $?

[jaredsampson]

Nope, not referenced there.

$ grep dri3proto ~/.linuxbrew/Homebrew/Library/Taps/linuxbrew/homebrew-xorg/Formula/xorgproto.rb

$ echo $?
1

[sjackman]

Try…

ls -d ~/.linuxbrew/Cellar/*proto

[JuPlutonic]

xcb-proto and xorgproto

Try…

ls -d ~/.linuxbrew/Cellar/*proto

And
grep dri3proto /opt/.linuxbrew/Homebrew/Library/Taps/linuxbrew/homebrew-xorg/Formula/xcb-proto.rb
echo $?
Is 1
brew-list.txt

[sjackman]

/move to Linuxbrew/homebrew-xorg

[move[bot]]

⚠️ The GitHub App must be installed for the target repository.

[move[bot]]

This issue was moved by sjackman to Linuxbrew/homebrew-xorg#452.