Linuxbrew-core: Attempting to install gtk+3 fails on atk dependency

Created on 13 Apr 2018 · 35Comments · Source: Homebrew/linuxbrew-core

Hi!

Trying to brew install gtk+3 fails with the error message No package 'atk' found. I can confirm that atk is in fact installed. Brew doctor yields ready to brew.

I came across this attempting to brew install amiaopensource/amiaos/ltopers but tracked it down to gtk+3 and atk. Attempting to brew install gtk+3 generates the problem.

Here's the requested gist: https://gist.github.com/mcampos-quinn/a748300c0a833f81278a2b4c428886fb

I see that there is an open pull request #6602 to create a linuxbrew bottle for gtk+3 and maybe this issue would be solved with that?

Thanks!

outdated

Source

mcampos-quinn

All 35 comments

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

stale[bot] on 4 May 2018

Same problem with gtk+ formula

arkanoid87 on 5 May 2018

👍1

What does this return for you?:

pkg-config --libs atk

iMichka on 5 May 2018

$ pkg-config --libs atk
Package atk was not found in the pkg-config search path.
Perhaps you should add the directory containing `atk.pc'
to the PKG_CONFIG_PATH environment variable
No package 'atk' found

2018-05-05 12:56 GMT+02:00 Michka Popoff notifications@github.com:

What does this return for you?:

pkg-config --libs atk

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arkanoid87 on 5 May 2018

Is brew in your path? Not sure the right pkg-config is being used here.
Can you try like this?

/home/linuxbrew/.linuxbrew/bin/pkg-config --libs atk

Also please provide your brew config. Thanks.

iMichka on 5 May 2018

$ which brew
~/.linuxbrew/bin/brew

$ which pkg-config
~/.linuxbrew/bin/pkg-config

$ $HOME/.linuxbrew/bin/pkg-config --libs atk
Package atk was not found in the pkg-config search path.
Perhaps you should add the directory containing `atk.pc'
to the PKG_CONFIG_PATH environment variable
No package 'atk' found

$ brew config
HOMEBREW_VERSION: >=1.4.0 (shallow or no git repository)
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: d9631dc889be0ce9731e3c07238fb1c2a1a06b4d
Last commit: 18 hours ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 10e4c1ccb5b2278617d2ffce5feb0425d7a7ba52
Core tap last commit: 12 minutes ago
HOMEBREW_PREFIX: /home/nfs/jack/.linuxbrew
HOMEBREW_REPOSITORY: /home/nfs/jack/.linuxbrew
HOMEBREW_CELLAR: /home/nfs/jack/.linuxbrew/Cellar
HOMEBREW_CACHE: /home/nfs/jack/.cache/Homebrew
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GITHUB_API_TOKEN: set
CPU: 20-core 64-bit haswell
Homebrew Ruby: 2.3.3 => /home/nfs/jack/.linuxbrew/Library/Homebrew/vendor/portable-ruby/2.3.3_2/bin/ruby
Clang: N/A
Git: 2.17.0 => /home/nfs/jack/.linuxbrew/bin/git
Curl: 7.29.0 => /usr/bin/curl
Java: N/A
Kernel: Linux 3.10.0-327.28.3.el7.x86_64 x86_64 GNU/Linux
OS: CentOS Linux release 7.2.1511 (Core)
Host glibc: 2.17
/usr/bin/gcc: 4.8.5
glibc: 2.23
gcc: 5.5.0_4
xorg: 20170115_1

arkanoid87 on 5 May 2018

brew list atk?

This should be there: lib/pkgconfig/atk.pc

iMichka on 5 May 2018

$ brew list atk
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/include/atk-1.0/ (34 files)
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/girepository-1.0/Atk-1.0.typelib
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/ (3 files)
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/share/gir-1.0/Atk-1.0.gir
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/share/locale/ (99 files)

arkanoid87 on 5 May 2018

Maybe this is because it is in a lib64 folder? I have:

/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/include/atk-1.0/ (34 files)
/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/lib/girepository-1.0/Atk-1.0.typelib
/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/lib/pkgconfig/atk.pc
/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/lib/ (3 files)
/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/share/gir-1.0/Atk-1.0.gir
/home/linuxbrew/.linuxbrew/Cellar/atk/2.28.1_2/share/locale/ (99 files)

Can you try:
brew uninstall atk && brew install atk?

iMichka on 5 May 2018

[jack@geo1 Formula]$ brew uninstall atk
Uninstalling /home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2... (145 files, 2.2MB)
[jack@geo1 Formula]$ brew install atk
Updating Homebrew...
==> Downloading https://download.gnome.org/sources/atk/2.28/atk-2.28.1.tar.xz
Already downloaded: /home/nfs/jack/.cache/Homebrew/atk-2.28.1.tar.xz
==> Patching
patching file meson.build
==> meson --prefix=/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2 ..
==> ninja
==> ninja install
🍺  /home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2: 145 files, 2.2MB, built in 30 seconds
[jack@geo1 Formula]$ $HOME/.linuxbrew/bin/pkg-config --libs atk
Package atk was not found in the pkg-config search path.
Perhaps you should add the directory containing `atk.pc'
to the PKG_CONFIG_PATH environment variable
No package 'atk' found
[jack@geo1 Formula]$ brew list atk
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/include/atk-1.0/ (34 files)
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/girepository-1.0/Atk-1.0.typelib
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64/ (3 files)
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/share/gir-1.0/Atk-1.0.gir
/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/share/locale/ (99 files)
[jack@geo1 Formula]$

arkanoid87 on 5 May 2018

Ok, so whatever we do, on your system it really wants to use a lib64dir. Not sure why.

The thing is, brew will just use stuff that is in a lib dir, if I am not mistaken. This means that everything else will not be recognised and sanitised away.

Could you try to add HOMEBREW_PREFIX/"lib64/pkgconfig", to this file?
https://github.com/Linuxbrew/brew/blob/99f86f148eeee7c4727e8ab358de21dcf53268f1/Library/Homebrew/extend/ENV/std.rb#L93

You may need to set export HOMEBREW_NO_AUTO_UPDATE=1 so that the change is not reset, and then try to install gtk+3 again.

It is just to confirm that this is the problem. Not saying that the change I propose here is the right way to fix it.

iMichka on 5 May 2018

👍1

.linuxbrew/Library/Homebrew/extend/ENV/std.rb

def determine_pkg_config_libdir
    PATH.new(
      HOMEBREW_PREFIX/"lib/pkgconfig",
      HOMEBREW_PREFIX/"lib64/pkgconfig",
      HOMEBREW_PREFIX/"share/pkgconfig",
      homebrew_extra_pkg_config_paths,
      *("/usr/lib/pkgconfig" if OS.mac?),
    ).existing
  end

$ HOMEBREW_NO_AUTO_UPDATE=1 brew install gtk+
==> Downloading https://download.gnome.org/sources/gtk+/2.24/gtk+-2.24.32.tar.xz
Already downloaded: /home/nfs/jack/.cache/Homebrew/gtk+-2.24.32.tar.xz
==> Downloading https://bug757187.bugzilla-attachments.gnome.org/attachment.cgi?id=331173
Already downloaded: /home/nfs/jack/.cache/Homebrew/gtk+--patch-ce5adf1a019ac7ed2a999efb65cfadeae50f5de8663638c7f765f8764aa7d931.cgi
==> Patching
==> Applying attachment.cgi
patching file gdk/quartz/gdkimage-quartz.c
==> ./configure --disable-silent-rules --prefix=/home/nfs/jack/.linuxbrew/Cellar/gtk+/2.24.32_2 --disable-glibtest --enable-introspection=yes --with-gdktarget=x11 --disable-visibility --disable
Last 15 lines from /home/nfs/jack/.cache/Homebrew/Logs/gtk+/01.configure:
checking for library containing strerror... none required
checking whether make sets $(MAKE)... (cached) yes
checking for pkg-config... /home/nfs/jack/.linuxbrew/opt/pkg-config/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for BASE_DEPENDENCIES... no
configure: error: Package requirements (glib-2.0 >= 2.28.0    atk >= 1.29.2    pango >= 1.20    cairo >= 1.6    gdk-pixbuf-2.0 >= 2.21.0) were not met:

No package 'atk' found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables BASE_DEPENDENCIES_CFLAGS
and BASE_DEPENDENCIES_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
gtk-doc: Build a bottle for Linuxbrew https://github.com/Linuxbrew/homebrew-core/pull/6929
Attempting to install gtk+3 fails on atk dependency https://github.com/Linuxbrew/homebrew-core/issues/7175
No package 'cairo-xlib' found in compiling gtk+(yocto) https://github.com/Linuxbrew/homebrew-core/issues/7199
[jack@geo1 Library]$

arkanoid87 on 5 May 2018

me too have trouble with gtk+ formula (see my reference with gist-logs).
pkg-config --libs atk
``Package atk was not found in the pkg-config search path. Perhaps you should add the directory containingatk.pc'
to the PKG_CONFIG_PATH environment variable
No package 'atk' found

brew list atk (after brew uninstall atk && brew install atk)

/opt/.linuxbrew/Cellar/atk/2.28.1_2/include/atk-1.0/ (34 files)
/opt/.linuxbrew/Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/ (5 files)
/opt/.linuxbrew/Cellar/atk/2.28.1_2/share/gir-1.0/Atk-1.0.gir
/opt/.linuxbrew/Cellar/atk/2.28.1_2/share/locale/ (99 files)

*atk.pc* can be found in

brew --repository/Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/pkgconfig
```

JuPlutonic on 6 May 2018

Added to L95

HOMEBREW_PREFIX/"lib64/pkgconfig",

Created directory

mkdir -p `brew --repository`/lib64/pkgconfig

creatred symlink ln -s $(brew --repository)/Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/pkgconfig/atk.pc $(brew --repository/lib64/pkgconfig/atk.pc
then run
HOMEBREW_NO_AUTO_UPDATE=1 brew install gtk+
and got same error with atk

JuPlutonic on 6 May 2018

@JuPlutonic I see that you are using Ubuntu 18.04. I do too, and I can not reproduce the error.

I think I have another idea. I was looking on how the pkg-config formula is working (https://github.com/Linuxbrew/homebrew-core/blob/master/Formula/pkg-config.rb#L19-L27).
We setup a path and tell pkg-config where to look for .pc files.

Can you execute the following command:
pkg-config pkg-config --variable pc_path

This will tell us where pkg-config is looking first. In my case, the first location is:
/home/linuxbrew/.linuxbrew/lib/pkgconfig
In there, you can find all the .pc files, which are symlinks to the original .pc file in the Cellar.

Can you check the first path is pointing to the right lib folder? Is the atk.pc file in there? Does it point to the right atk.pc file in Cellar?

I also see this x86_64-linux-gnu subfolder in lib/x86_64-linux-gnu/pkgconfig/atk.pc, and not sure from where it comes from? I tried to rebuild pkg-config and atk from source to see if that folder pops up, but I do not see that happen, so I am wondering why it exists at all, and if this is why everything is messed up for you.

iMichka on 6 May 2018

1st command gave /opt/.linuxbrew/lib/pkgconfig:/opt/.linuxbrew/share/pkgconfig:/opt/.linuxbrew/Library/Homebrew/os/linux/pkgconfig
/opt/.linuxbrew is mine repository
/opt/.linuxbrew/lib/pkgconfig doesn't contain atk.pc symlink (but brew linkage --test atk didn't report about that).
/opt/.linuxbrew/share/pkgconfig contains only 8 symlinks
and path /opt/.linuxbrew/Library/Homebrew/os/linux/pkgconfig doesn't exist.

JuPlutonic on 6 May 2018

/opt/.linuxbrew/lib/x86_64-linux-gnu (is symlink) -> ../Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu is where actually pkgconfig/atk.pc located.
This path not in Library/Taps/homebrew/homebrew-core/Formula/pkg-config.rb
and not in Library/std.rbHomebrew/extend/ENV/std.rb.
I need to cp lib64/pkgconfig/atk.pc to lib/pkgconfig/atk.pc or add line #{HOMEBREW_PREFIX}/lib64/pkgconfig to https://github.com/Linuxbrew/homebrew-core/blob/master/Formula/pkg-config.rb#L20. To get working gtk installation.
But better is after *L27 put pc_path << "#{HOMEBREW_PREFIX}/lib/x86_64-linux-gnu/pkgconfig" if File.exists? File.expand_path("#{HOMEBREW_PREFIX}/lib/x86_64-linux-gnu/pkgconfig")
And I think what we don't need to create lib64 and change atk formula.

JuPlutonic on 6 May 2018

Here's my pc_path. It is not containing atk.pc

[jack@geo1 .linuxbrew]$ pkg-config pkg-config --variable pc_path
/home/nfs/jack/.linuxbrew/lib/pkgconfig:/home/nfs/jack/.linuxbrew/share/pkgconfig:/home/nfs/jack/.linuxbrew/Library/Homebrew/os/linux/pkgconfig
[jack@geo1 .linuxbrew]$ find . -name atk.pc
./Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc

arkanoid87 on 6 May 2018

Ok so to summarise:
pkg-config pkg-config --variable pc_path gives for both of you something like
/mypath/.linuxbrew/lib/pkgconfig:/mypath/.linuxbrew/share/pkgconfig:/mypath/.linuxbrew/Library/Homebrew/os/linux/pkgconfig

This is fine.

But then you have one of these possibilities for the atk.pc file:

Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/pkgconfig/atk.pc
Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc

The proposed fix is to add:

pc_path << "#{HOMEBREW_PREFIX}/lib/x86_64-linux-gnu" if File.exists?
pc_path << "#{HOMEBREW_PREFIX}/lib64" if File.exists?

to the pkg-config formula.

@sjackman Have you already seen this problem?

iMichka on 6 May 2018

Actually we need also to get rid of the #{HOMEBREW_LIBRARY}/Homebrew/os/linux/pkgconfig path as it does not exist anymore, but I do not believe this is why we are getting errors here.

iMichka on 6 May 2018

I think #{HOMEBREW_LIBRARY}/Homebrew/os/linux/pkgconfig exists simply for parallelism with Brew on macOS, but this directoy has never existed. I'm fine to remove it.

Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/pkgconfig/atk.pc
Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc

Ideally this file would be moved to Cellar/atk/2.28.1_2/lib/pkgconfig/atk.pc. As a workaround, I'm okay with adding Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/pkgconfig to the search path.

sjackman on 6 May 2018

in my case #{HOMEBREW_LIBRARY}/lib/pkgconfig exists and contains many symlinks to pc files, but not atk.pc

arkanoid87 on 6 May 2018

I've tried to create manually atk.pc link

$ pwd
/home/nfs/jack/.linuxbrew/lib/pkgconfig
$ ls -lah atk.pc
lrwxrwxrwx. 1 jack jack 48 May  6 21:54 atk.pc -> ../../Cellar/atk/2.28.1_2/lib64/pkgconfig/atk.pc

now pkg-config seems to work

$ pkg-config --list-all | grep atk
atk                                 Atk - Accessibility Toolkit
pkg-config --libs atk.pc
-L/home/nfs/jack/.linuxbrew/Cellar/atk/2.28.1_2/lib64 -L/home/nfs/jack/.linuxbrew/Cellar/glib/2.56.1/lib -latk-1.0 -lgobject-2.0 -lglib-2.0

but gtk+ install keep failing

[jack@geo1 pkgconfig]$ brew install gtk+
Updating Homebrew...
==> Downloading https://download.gnome.org/sources/gtk+/2.24/gtk+-2.24.32.tar.xz
Already downloaded: /home/nfs/jack/.cache/Homebrew/gtk+-2.24.32.tar.xz
==> Downloading https://bug757187.bugzilla-attachments.gnome.org/attachment.cgi?id=331173
Already downloaded: /home/nfs/jack/.cache/Homebrew/gtk+--patch-ce5adf1a019ac7ed2a999efb65cfadeae50f5de8663638c7f765f8764aa7d931.cgi
==> Patching
==> Applying attachment.cgi
patching file gdk/quartz/gdkimage-quartz.c
==> ./configure --disable-silent-rules --prefix=/home/nfs/jack/.linuxbrew/Cellar/gtk+/2.24.32_2 --disable-glibtest --enable-introspection=yes --with-gdktarget=x11 --disable-visibility --disable
Last 15 lines from /home/nfs/jack/.cache/Homebrew/Logs/gtk+/01.configure:
checking for library containing strerror... none required
checking whether make sets $(MAKE)... (cached) yes
checking for pkg-config... /home/nfs/jack/.linuxbrew/opt/pkg-config/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for BASE_DEPENDENCIES... no
configure: error: Package requirements (glib-2.0 >= 2.28.0    atk >= 1.29.2    pango >= 1.20    cairo >= 1.6    gdk-pixbuf-2.0 >= 2.21.0) were not met:

No package 'atk' found

arkanoid87 on 6 May 2018

Any news on this? I am failing in finding even the simplest workaround

arkanoid87 on 7 May 2018

Good to know that adding the symlink moved us a little bit forward. I think I will add some changes to brew and to the pkg-config formula to make this work. I’ll try to work on this today or tomorrow.

https://unix.stackexchange.com/questions/43190/where-did-usr-lib64-go-and-what-is-usr-lib-x86-64-linux-gnu

Reading this, it seems that we will need to support three types of folder layouts (lib, lib64, lib/x86-64-linux-gnu). And maybe more if needed.

I am still wondering who is deciding where to put stuff when atk is installed. Maybe it is make? As you all probably use your system’s make, this may explain the differences.

iMichka on 8 May 2018

Another solution is to move files from these 64-bit specific library directories to lib, since Linuxbrew does not support multilib.

sjackman on 9 May 2018

👍1

I found problem with atk when using linuxbrew's python3.6.5 or ubuntu beaver's python3.6.5:

/opt/.linuxbrew/bin/python3:
Python 3.6.5 (default, Apr 3 2018, 15:18:52)
[GCC 5.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import gi
gi.require_version("Gtk", "3.0")
Traceback (most recent call last):
File "", line 1, in
File "/opt/.linuxbrew/Cellar/python/3.6.5/lib/python3.6/site-packages/gi/__init__.py", line 134, in require_version
(namespace, version))
ValueError: Namespace Gtk not available for version 3.0
from gi import Repository
r = Repository.get_default()
r.require('Gtk')
Traceback (most recent call last):
File "", line 1, in
gi.RepositoryError: Typelib file for namespace 'Atk', version '1.0' not found

/usr/bin/python3:
Python 3.6.5 (default, Apr 1 2018, 05:46:30)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import gi
gi.require_version("Gtk", "3.0")
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python3/dist-packages/gi/__init__.py", line 134, in require_version
(namespace, version))
ValueError: Namespace Gtk not available for version 3.0
from gi import Repository
r = Repository.get_default()
r.require('Gtk') # See note about versions
Traceback (most recent call last):
File "", line 1, in
gi.RepositoryError: Typelib file for namespace 'Atk', version '1.0' not found

brew linkage --test atk    -> 
Unwanted system libraries:
  libglib-2.0.so.0
  libgobject-2.0.so.0


pkg-config --libs atk   ->
-L/opt/.linuxbrew/Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu -L/opt/.linuxbrew/Cellar/glib/2.56.1/lib -latk-1.0 -lgobject-2.0 -lglib-2.0

JuPlutonic on 14 May 2018

@arkanoid87 After I copied all from lib64 (x86_64-linux-gnu in my case):

cp -R `brew --repository`/Cellar/atk/2.28.1_2/lib/x86_64-linux-gnu/* `brew --repository`/Cellar/atk/2.28.1_2/lib

@iMichka got another error (gist-file) so may be we need to fix atk / at-sp2-atk to get gtk+3 installation / bottling working?

JuPlutonic on 14 May 2018

After I copied

cp -R cp -R `brew --repository`/Cellar/at-spi2-core/2.28.0/lib/x86_64-linux-gnu/* cp -R `brew --repository`/Cellar/at-spi2-core/2.28.0/lib

I finally got gtk+ installed.

JuPlutonic on 14 May 2018

@sjackman on your last comment.
Do we need to change Linuxbrew/homebrew-core/blob/master/Formula/pkg-config.rb and other env related tricks or change Linuxbrew/homebrew-core or Homebrew/homebrew-core to install not to lib/x86_64-linux-gnu?
There such problems with formulas

at-spi2-core
atk

JuPlutonic on 14 May 2018

I found an (untested) solution: meson seems to accept a path for the libdir. We could modify the atk formula like this:
meson --libdir=pathtoinstallprerfix/lib

I need to test this but it may be a solution, as it will force the installation in the lib folder.

iMichka on 14 May 2018

👍1

Here is the a possible fix: #7663

Can somebody check if this works?

iMichka on 14 May 2018

@iMichka, yes, works.
brew install --build-from-source /opt/.linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/atk.rb

==> Downloading https://download.gnome.org/sources/atk/2.28/atk-2.28.1.tar.xz
Already downloaded: /home/salessionato/.cache/Homebrew/atk-2.28.1.tar.xz
==> Patching
patching file meson.build
==> meson --prefix=/opt/.linuxbrew/Cellar/atk/2.28.1_2 --libdir=/opt/.linuxbrew/
==> ninja
==> ninja install
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /opt/.linuxbrew
Could not symlink lib/pkgconfig/atk.pc
Target /opt/.linuxbrew/lib/pkgconfig/atk.pc
already exists. You may want to remove it:
  rm '/opt/.linuxbrew/lib/pkgconfig/atk.pc'

To force the link and overwrite all conflicting files:
  brew link --overwrite atk

To list all files that would be deleted:
  brew link --overwrite --dry-run atk

Possible conflicting files are:
/opt/.linuxbrew/lib/pkgconfig/atk.pc
==> Summary
/opt/.linuxbrew/Cellar/atk/2.28.1_2: 145 files, 3MB, built in 21 seconds

brew link --overwrite --dry-run atk

Would remove:
/opt/.linuxbrew/lib/pkgconfig/atk.pc

JuPlutonic on 15 May 2018

@JuPlutonic Consider installing Linuxbrew in /home/linuxbrew/.linuxbrew/ if possible so that you can use precompiled binary packages (known as bottles) for non-relocatable formula like atk.
Another possible workaround for you is brew install --force-bottle atk, but no promises.

If it's an option for you, you could open a ticket with your information systems department to ask that they create a linuxbrew role account with home directory /home/linuxbrew.

The precompiled binary bottles of non-relocatable bottles can only be used if you install in /home/linuxbrew/.linuxbrew, otherwise they have to be built from source. See the documentation below. On macOS the default installation directory is /usr/local. On Linux the default installation directory is /home/linuxbrew/.linuxbrew.