brew update : Bad file descriptor (Errno::EBADF)

Created on 18 May 2016 · 26Comments · Source: Homebrew/brew

[x] Ran brew update and retried your prior step?
[x] Ran brew doctor, fixed as many issues as possible and retried your prior step?
[x] If you're seeing permission errors tried running sudo chown -R $(whoami) $(brew --prefix)?

Bug reports:

brew update fails.

steps taken
[1] ls -la $(brew --prefix)

drwxrwxr-x  19 ram   admin   646 May 16 00:12 .
drwxr-xr-x@ 13 root  wheel   442 May 15 17:17 ..
drwxr-xr-x  14 ram   admin   476 May 18 22:57 .git
drwxr-xr-x   5 ram   admin   170 May 15 17:18 .github
-rw-r--r--   1 ram   admin  1016 May 15 17:18 .gitignore
-rw-r--r--   1 ram   admin   861 May 15 17:18 .travis.yml
-rw-r--r--   1 ram   admin   291 May 15 17:18 .yardopts
-rw-r--r--   1 ram   admin  3161 May 15 17:18 CODEOFCONDUCT.md
drwxr-xr-x  11 ram   admin   374 May 16 00:39 Cellar
-rw-r--r--   1 ram   admin  1241 May 15 17:18 LICENSE.txt
drwxr-xr-x  11 ram   admin   374 May 15 17:32 Library
-rw-r--r--   1 ram   admin  3918 May 15 17:18 README.md
drwxr-xr-x  94 ram   admin  3196 May 18 22:50 bin
drwxr-xr-x   5 ram   admin   170 May 16 00:36 etc
drwxr-xr-x   4 ram   admin   136 May 16 00:31 include
drwxr-xr-x  12 ram   admin   408 May 16 00:31 lib
drwxr-xr-x  11 ram   admin   374 May 16 00:39 opt
drwxr-xr-x  16 ram   admin   544 May 17 20:27 share
drwxr-xr-x   5 ram   admin   170 May 16 00:36 var

[2] 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 and just ignore them. Thanks!

Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.

[3] brew update

-e:1:in `initialize': Bad file descriptor (Errno::EBADF)
    from -e:1:in `new'
    from -e:1:in `<main>'
Error: Another active Homebrew process is already in progress.
Please wait for it to finish or terminate it to continue.

Source

ramonrails

Most helpful comment

I had the same issue, my problem was that I run a sudo command that probably affected some permissions, so to fix Homebrew I first run the following command to fix the permissions:

sudo chown -R "$USER":admin /usr/local

After that I did a cleanup:

brew cleanup

And I was successfully able to update Homebrew and install packages.
Hope this helps!

rochastuff on 22 Sep 2016

👍32 🎉1

All 26 comments

Try to cd /usr/local; git reset --hard origin/master; brew update.

CC @xu-cheng for what looks like a locking bug.

MikeMcQuaid on 18 May 2016

👍1

Can you show the output of ls -al /tmp/

xu-cheng on 18 May 2016

output is (relevant pasted here only)

drwxrwxrwt  12 root  wheel  408 May 18 23:12 .
drwxr-xr-x@  6 root  wheel  204 May 15 14:58 ..
-rw-r--r--   1 ram   wheel    0 May 18 23:08 homebrew-usr-local-update.lock

FIX: I just restarted the terminal. brew updated correctly. You may close this
please. I do understand that I have to remove this lock file too, just in case. Thank you.

ramonrails on 18 May 2016

@ramonrails Were you using tmux or screen or anything? The output of ls -al /tmp/ would still be useful if you can provide it so we can avoid others hitting this issue. Thanks!

MikeMcQuaid on 18 May 2016

@mikemcquaid I just did. the relevant part only, though. thank you.

ramonrails on 18 May 2016

@ramonrails Thanks!

MikeMcQuaid on 18 May 2016

This came again Today. Here are the complete output and steps.

brew doctor is clean

ruby-2.3.1 ~/work/projects/code/sso (develop)*$ brew doctor
Your system is ready to brew.

brew update complained about another process (I only had single terminal console open.

ruby-2.3.1 ~/work/projects/code/sso (develop)*$ brew update
-e:1:in `initialize': Bad file descriptor (Errno::EBADF)
    from -e:1:in `new'
    from -e:1:in `<main>'
Error: Another active Homebrew process is already in progress.
Please wait for it to finish or terminate it to continue.

I looked at the /tmp folder as suggested above

ruby-2.3.1 ~/work/projects/code/sso (develop)*$ ll /tmp/
total 8
drwxrwxrwt  12 root  wheel   408B May 19 13:03 ./
drwxr-xr-x@  6 root  wheel   204B May 15 14:58 ../
-rw-rw-rw-   1 ram   wheel     0B May 19 12:53 .keystone_install_lock
drwx------   3 ram   wheel   102B May 19 12:53 KSOutOfProcessFetcher.501.ppfIhqX0vjaTSb8AJYobDV7Cu68=/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.LVqVic1quK/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.UhC06p2CBa/
-rw-r--r--@  1 ram   wheel     0B May 19 12:53 ct.shutdown
-rw-r--r--   1 ram   wheel     0B May 19 13:03 homebrew-usr-local-update.lock
srwx------   1 ram   wheel     0B May 19 12:53 mongodb-27017.sock
srwxrwxrwx   1 ram   wheel     0B May 19 12:53 mysql.sock
-rw-------   1 ram   wheel     4B May 19 12:53 mysql.sock.lock
srwxr-xr-x   1 ram   wheel     0B May 19 12:57 textmate-501.sock

found home-brew-.... lock file, removed it.

ruby-2.3.1 ~/work/projects/code/sso (develop)*$ rm /tmp/homebrew-usr-local-update.lock 
ruby-2.3.1 ~/work/projects/code/sso (develop)*$ ll /tmp/
total 8
drwxrwxrwt  11 root  wheel   374B May 19 13:04 ./
drwxr-xr-x@  6 root  wheel   204B May 15 14:58 ../
-rw-rw-rw-   1 ram   wheel     0B May 19 12:53 .keystone_install_lock
drwx------   3 ram   wheel   102B May 19 12:53 KSOutOfProcessFetcher.501.ppfIhqX0vjaTSb8AJYobDV7Cu68=/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.LVqVic1quK/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.UhC06p2CBa/
-rw-r--r--@  1 ram   wheel     0B May 19 12:53 ct.shutdown
srwx------   1 ram   wheel     0B May 19 12:53 mongodb-27017.sock
srwxrwxrwx   1 ram   wheel     0B May 19 12:53 mysql.sock
-rw-------   1 ram   wheel     4B May 19 12:53 mysql.sock.lock
srwxr-xr-x   1 ram   wheel     0B May 19 12:57 textmate-501.sock

brew update failed anyways. the lock file was also re-created somehow during the brew update command

ruby-2.3.1 ~/work/projects/code/sso (develop)*$ brew update
-e:1:in `initialize': Bad file descriptor (Errno::EBADF)
    from -e:1:in `new'
    from -e:1:in `<main>'
Error: Another active Homebrew process is already in progress.
Please wait for it to finish or terminate it to continue.
ruby-2.3.1 ~/work/projects/code/sso (develop)*$ ll /tmp/
total 8
drwxrwxrwt  11 root  wheel   374B May 19 13:05 ./
drwxr-xr-x@  6 root  wheel   204B May 15 14:58 ../
-rw-rw-rw-   1 ram   wheel     0B May 19 12:53 .keystone_install_lock
drwx------   3 ram   wheel   102B May 19 12:53 KSOutOfProcessFetcher.501.ppfIhqX0vjaTSb8AJYobDV7Cu68=/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.LVqVic1quK/
drwx------   3 ram   wheel   102B May 19 12:53 com.apple.launchd.UhC06p2CBa/
-rw-r--r--@  1 ram   wheel     0B May 19 12:53 ct.shutdown
-rw-r--r--   1 ram   wheel     0B May 19 13:04 homebrew-usr-local-update.lock
srwx------   1 ram   wheel     0B May 19 12:53 mongodb-27017.sock
srwxrwxrwx   1 ram   wheel     0B May 19 12:53 mysql.sock
-rw-------   1 ram   wheel     4B May 19 12:53 mysql.sock.lock

_PS: I was not sure whether to create a new issue or re-open this one. So, I just posted here on the closed issue @mikemcquaid @xu-cheng thank you for looking into this. Meanwhile, I will just reinstall home-brew fresh again to see if this goes away._

ramonrails on 19 May 2016

May I ask the output of which ruby? Are you using rbenv or RVM?

xu-cheng on 19 May 2016

rbenv 1.0.0
/Users/ram/.rbenv/shims/ruby

ramonrails on 19 May 2016

What's the output of rbenv which ruby and rbenv version?

xu-cheng on 19 May 2016

ruby-2.3.1 ~ $ rbenv which ruby
/Users/ram/.rbenv/versions/2.3.1/bin/ruby

ruby-2.3.1 ~ $ rbenv version
2.3.1 (set by /Users/ram/.rbenv/version)

ramonrails on 19 May 2016

I have the exact same problem, running brew update gives

Errno::EBADF: Bad file descriptor - Bad file descriptor
  initialize at org/jruby/RubyIO.java:923
  initialize at org/jruby/RubyFile.java:362
         new at org/jruby/RubyIO.java:853
      (root) at -e:1
Error: Another active Homebrew process is already in progress.

I'm using rvm, outputs of aforeasked

which ruby
/Users/ahtikatiska/.rvm/rubies/jruby-1.7.23/bin/ruby

rvm which ruby
/Users/ahtikatiska/.rvm/rubies/jruby-1.7.23/bin/ruby

rvm version
rvm 1.27.0 (latest) by Wayne E. Seguin <[email protected]>, Michal Papis <[email protected]> [https://rvm.io/]

Also tried removing the .lock file that the brew update creates, no change. Closed all terminals, no change. Rebooted system, no change.

TetsuHari on 23 May 2016

@ramonrails @KatsCyl

In order to help me debug this, could you show the output for following commands run in Bash?

brew config
brew doctor
ls -al /dev/fd/
exec 200>/tmp/test.lock
ls -al /dev/fd/
ruby -e 'File.new(200)'

Also have you set Bash in restricted mode or other non-standard mode?

xu-cheng on 23 May 2016

brew config
HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Homebrew/brew
HEAD: 2f20a42292e7d8d8f9ae9286632155a46e599700
Last commit: 8 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 0a6ddaa2dce2a03675f9296d7fafc98278a73cbc
Core tap last commit: 7 days ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: 8-core 64-bit haswell
Clang: 7.3 build 703
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /Users/ahtikatiska/.rvm/rubies/jruby-1.7.23/bin/ruby => /Users/ahtikatiska/.rvm/rubies/jruby-1.7.23/bin/jruby
Java: 1.8.0_92, 1.8.0_91
System Ruby: 2.0.0-p648
OS X: 10.11.5-x86_64
Xcode: N/A
CLT: 7.3.1.0.1.1461711523
X11: N/A

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 and just ignore them. Thanks!

Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.

ls -al /dev/fd/
total 0
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:31 0
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:31 1
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:31 2
drw-r--r--  36 ahtikatiska  staff      1224 May 23 13:48 3
dr--r--r--   1 root         wheel         0 May 23 14:39 4

exec 200>/tmp/test.lock

ls -al /dev/fd/
total 0
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:32 0
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:32 1
crw--w----   1 ahtikatiska  tty     16,   0 May 23 15:32 2
-rw-r--r--   1 ahtikatiska  wheel         0 May 23 15:32 200
drw-r--r--  36 ahtikatiska  staff      1224 May 23 13:48 3
dr--r--r--   1 root         wheel         0 May 23 14:39 4

ruby -e 'File.new(200)'
Errno::EBADF: Bad file descriptor - Bad file descriptor
  initialize at org/jruby/RubyIO.java:923
  initialize at org/jruby/RubyFile.java:362
         new at org/jruby/RubyIO.java:853
      (root) at -e:1

And I don't believe that my bash is in any non-standard mode.

TetsuHari on 23 May 2016

ruby-2.3.1 ~/tmp $ brew config
HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Homebrew/brew
HEAD: d345483de164e062727f95d3fbd575433d735548
Last commit: 16 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 6442c12aea41de740333aff8249cc3c09fb1dd9e
Core tap last commit: 10 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: 8-core 64-bit ivybridge
Clang: 7.3 build 703
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /Users/ram/.rbenv/shims/ruby => /Users/ram/.rbenv/versions/2.3.1/bin/ruby
Java: N/A
System Ruby: 2.0.0-p648
OS X: 10.11.4-x86_64
Xcode: 7.3.1
CLT: 7.3.1.0.1.1461711523
X11: N/A

ruby-2.3.1 ~/tmp $ brew doctor
Your system is ready to brew.

ruby-2.3.1 ~/tmp $ ls -al /dev/fd/
total 0
crw--w----  1 ram   tty     16,   2 May 23 18:17 0
crw--w----  1 ram   tty     16,   2 May 23 18:17 1
crw--w----  1 ram   tty     16,   2 May 23 18:17 2
drw-r--r--  5 ram   staff       170 May 22 23:41 3
dr--r--r--  1 root  wheel         0 May 23 11:52 4

ruby-2.3.1 ~/tmp $ exec 200>/tmp/test.lock

ruby-2.3.1 ~/tmp $ ls -al /dev/fd/
total 0
crw--w----  1 ram   tty     16,   2 May 23 18:18 0
crw--w----  1 ram   tty     16,   2 May 23 18:18 1
crw--w----  1 ram   tty     16,   2 May 23 18:18 2
-rw-r--r--  1 ram   wheel         0 May 23 18:18 200
drw-r--r--  5 ram   staff       170 May 22 23:41 3
dr--r--r--  1 root  wheel         0 May 23 11:52 4

ruby-2.3.1 ~/tmp $ ruby -e 'File.new(200)'
ruby-2.3.1 ~/tmp $

FYI, I had the privilege and therefore did a complete uninstall and reinstall of homebrew, rbenv, ruby. After that, this error came once only.

ramonrails on 23 May 2016

@ramonrails It seems that error has been gone for you.

@KatsCyl Can you try:

exec 200>/tmp/test.lock
/usr/bin/ruby -e 'File.new(200)'

xu-cheng on 23 May 2016

That completed without errors

TetsuHari on 23 May 2016

As I explained above, I just needed to move on with my work, so reinstalled everything. Thank you for your time & attention to this issue @xu-cheng .

ramonrails on 23 May 2016

@MikeMcQuaid It seems that this bug comes from third party ruby interpreter. Shall we hardcore the path to /usr/bin/ruby, i.e. system ruby?

xu-cheng on 23 May 2016

@xu-cheng Seems like a good idea for now on OS X and then it can use the vendored Ruby when that exists.

MikeMcQuaid on 23 May 2016

@MikeMcQuaid Since I have no Mac access in this week, would you mind to open the PR?

As for vendor Ruby, I think we can keep to use system Ruby because this one line command is Ruby 1.x compatible. And we will use this lock when installing vendor Ruby.

xu-cheng on 23 May 2016

@xu-cheng done in https://github.com/Homebrew/brew/pull/271

MikeMcQuaid on 23 May 2016

I had the same issue, my problem was that I run a sudo command that probably affected some permissions, so to fix Homebrew I first run the following command to fix the permissions:

sudo chown -R "$USER":admin /usr/local

After that I did a cleanup:

brew cleanup

And I was successfully able to update Homebrew and install packages.
Hope this helps!

rochastuff on 22 Sep 2016

👍32 🎉1

@rochastuff helped me!