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Brew Doctor cause segfault. #4951

Closed Tchakatak closed 6 years ago

Tchakatak commented 6 years ago

Please note 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.

To help us debug your issue please explain:

I was simply running a brew doctor.

A simple brew doctor is enough to reproduce.

---- Brew CONFIG ----

HOMEBREW_VERSION: 1.7.5-40-g1ff42f9 ORIGIN: https://github.com/Homebrew/brew HEAD: 1ff42f90586a5f600aa34b9edf8f8e842f2fc461 Last commit: 15 hours ago Core tap ORIGIN: https://github.com/Homebrew/homebrew-core Core tap HEAD: 70414410188e2b9d419cf90554835fa6f8e499df Core tap last commit: 10 hours ago HOMEBREW_PREFIX: /usr/local HOMEBREW_DEV_CMD_RUN: 1 HOMEBREW_GIT: git CPU: octa-core 64-bit haswell Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby Clang: 10.0 build 1000 Git: 2.19.0 => /usr/local/bin/git Curl: 7.54.0 => /usr/bin/curl Java: 1.8.0_91 macOS: 10.13.6-x86_64 CLT: 10.0.0.0.1.1535735448 CLT headers: N/A Xcode: 10.0 XQuartz: 2.7.11 => /opt/X11

--- Brew DOCTOR --- /usr/local/Homebrew/Library/Homebrew/cache_store.rb:30: [BUG] Segmentation fault at 0x00007f8a687ffffe ruby 2.3.7p456 (2018-03-28 revision 63024) [universal.x86_64-darwin17]

-- Crash Report log information -------------------------------------------- See Crash Report log file under the one of following:

-- Control frame information ----------------------------------------------- c:0022 p:---- s:0120 e:000119 CFUNC :[] c:0021 p:0027 s:0116 e:000115 METHOD /usr/local/Homebrew/Library/Homebrew/cache_store.rb:30 c:0020 p:0014 s:0112 e:000111 METHOD /usr/local/Homebrew/Library/Homebrew/linkage_cache_store.rb:21 c:0019 p:0040 s:0109 e:000108 METHOD /usr/local/Homebrew/Library/Homebrew/linkage_cache_store.rb:51 c:0018 p:0042 s:0105 e:000104 METHOD /usr/local/Homebrew/Library/Homebrew/linkage_checker.rb:84 c:0017 p:0187 s:0097 E:001a68 METHOD /usr/local/Homebrew/Library/Homebrew/linkage_checker.rb:25 [FINISH] c:0016 p:---- s:0089 e:000088 CFUNC :new c:0015 p:0019 s:0083 e:000082 BLOCK /usr/local/Homebrew/Library/Homebrew/formula.rb:1790 c:0014 p:0024 s:0079 e:000078 METHOD /usr/local/Homebrew/Library/Homebrew/cache_store.rb:16 c:0013 p:0038 s:0073 e:000072 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1789 c:0012 p:0076 s:0068 e:000066 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1562 c:0011 p:0012 s:0059 e:000058 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1568 c:0010 p:0022 s:0053 e:000052 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1584 c:0009 p:0011 s:0048 e:000047 BLOCK /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13 [FINISH] c:0008 p:---- s:0044 e:000043 CFUNC :each c:0007 p:0019 s:0041 e:000040 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12 c:0006 p:0060 s:0035 e:000034 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652 c:0005 p:0085 s:0031 e:000030 BLOCK /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46 [FINISH] c:0004 p:---- s:0027 e:000026 CFUNC :each c:0003 p:0167 s:0024 e:000023 METHOD /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38 c:0002 p:0704 s:0017 E:0011b8 EVAL /usr/local/Homebrew/Library/Homebrew/brew.rb:91 [FINISH] c:0001 p:0000 s:0002 E:000920 (none) [FINISH]

-- Ruby level backtrace information ---------------------------------------- /usr/local/Homebrew/Library/Homebrew/brew.rb:91:in <main>' /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:indoctor' /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:in each' /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46:inblock in doctor' /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652:in check_missing_deps' /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:inmissing_deps' /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:in each' /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13:inblock in missing_deps' /usr/local/Homebrew/Library/Homebrew/formula.rb:1584:in missing_dependencies' /usr/local/Homebrew/Library/Homebrew/formula.rb:1568:inruntime_formula_dependencies' /usr/local/Homebrew/Library/Homebrew/formula.rb:1562:in runtime_dependencies' /usr/local/Homebrew/Library/Homebrew/formula.rb:1789:inundeclared_runtime_dependencies' /usr/local/Homebrew/Library/Homebrew/cache_store.rb:16:in use' /usr/local/Homebrew/Library/Homebrew/formula.rb:1790:inblock in undeclared_runtime_dependencies' /usr/local/Homebrew/Library/Homebrew/formula.rb:1790:in new' /usr/local/Homebrew/Library/Homebrew/linkage_checker.rb:25:ininitialize' /usr/local/Homebrew/Library/Homebrew/linkage_checker.rb:84:in check_dylibs' /usr/local/Homebrew/Library/Homebrew/linkage_cache_store.rb:51:infetch_type' /usr/local/Homebrew/Library/Homebrew/linkage_cache_store.rb:21:in keg_exists?' /usr/local/Homebrew/Library/Homebrew/cache_store.rb:30:inget' /usr/local/Homebrew/Library/Homebrew/cache_store.rb:30:in `[]'

-- Machine register context ------------------------------------------------ rax: 0x00007f8a681dd790 rbx: 0x0000000000000000 rcx: 0x00007f8a68800000 rdx: 0x0000000000000000 rdi: 0x0000000000000007 rsi: 0x0000000000001000 rbp: 0x00007ffee33c87e0 rsp: 0x00007ffee33c87c0 r8: 0x0000000000000002 r9: 0x0000000000000000 r10: 0x000000000015a000 r11: 0x0000000000000206 r12: 0x00007f8a681ce620 r13: 0x0000000000001000 r14: 0x00007ffee33c8810 r15: 0x00007f8a681ce620 rip: 0x00007fff57cd4918 rfl: 0x0000000000010212

-- C level backtrace information ------------------------------------------- 0 Ruby 0x00007fff3b55f080 rb_print_backtrace + 29 1 Ruby 0x00007fff3b55f257 rb_vm_bugreport + 364 2 Ruby 0x00007fff3b45b400 rb_bug_context + 206 3 Ruby 0x00007fff3b4f735a Init_signal + 3242 4 libsystem_platform.dylib 0x00007fff57f7bf5a _sigtramp + 26 5 libsystem_c.dylib 0x00007fff57cd4918 __find_last_page + 55 6 libsystem_c.dylib 0x00007fff57cd41cb hash_access + 319 7 libsystem_c.dylib 0x00007fff57cd6ac2 dbm_fetch + 31 8 dbm.bundle 0x000000010ca62859 Init_dbm + 6570 9 Ruby 0x00007fff3b55779a rb_vm_fstring_table + 5381 10 Ruby 0x00007fff3b54c2a5 rb_vm_get_insns_address_table + 20061 11 Ruby 0x00007fff3b553c05 rb_iseq_eval + 412 12 Ruby 0x00007fff3b55c9cb rb_vm_fstring_table + 26422 13 Ruby 0x00007fff3b54e8b1 rb_funcallv + 224 14 Ruby 0x00007fff3b4a45cb rb_class_new_instance + 41 15 Ruby 0x00007fff3b55779a rb_vm_fstring_table + 5381 16 Ruby 0x00007fff3b549006 rb_vm_get_insns_address_table + 7102 17 Ruby 0x00007fff3b553c05 rb_iseq_eval + 412 18 Ruby 0x00007fff3b550e65 rb_yield_1 + 75 19 Ruby 0x00007fff3b42e40a rb_ary_each + 51 20 Ruby 0x00007fff3b55779a rb_vm_fstring_table + 5381 21 Ruby 0x00007fff3b548f30 rb_vm_get_insns_address_table + 6888 22 Ruby 0x00007fff3b553c05 rb_iseq_eval + 412 23 Ruby 0x00007fff3b550e65 rb_yield_1 + 75 24 Ruby 0x00007fff3b42e40a rb_ary_each + 51 25 Ruby 0x00007fff3b55779a rb_vm_fstring_table + 5381 26 Ruby 0x00007fff3b548f30 rb_vm_get_insns_address_table + 6888 27 Ruby 0x00007fff3b553c05 rb_iseq_eval + 412 28 Ruby 0x00007fff3b45fe92 ruby_exec_node + 232 29 Ruby 0x00007fff3b45fd85 ruby_run_node + 39 30 ruby 0x000000010c8361bd main + 98

-- Other runtime information -----------------------------------------------

[NOTE] You may have encountered a bug in the Ruby interpreter or extension libraries. Bug reports are welcome. For details: http://www.ruby-lang.org/bugreport.html

[1] 7927 abort brew doctor

MikeMcQuaid commented 6 years ago

HOMEBREW_VERSION: 1.7.5-40-g1ff42f9 ORIGIN: https://github.com/Homebrew/brew HEAD: 1ff42f9

Please run brew update and try again. This should be fixed but I'll reopen this or another issue if not.

ansonhoyt commented 6 years ago

This is still happening for me with Homebrew 1.7.6.

This looks this same as https://github.com/Homebrew/homebrew-core/issues/32255

brew config

HOMEBREW_VERSION: 1.7.6-9-g2ea3aee
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 2ea3aee461f4b2f22ccc9b6f72b4426448bc1039
Last commit: 5 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7a8d0b66d5e62ba80d3f545083b850306b17c57e
Core tap last commit: 18 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 1.8.0_72, 1.6.0_33-b03-424, 1.6.0_29-b11-402
macOS: 10.13.6-x86_64
CLT: 9.4.0.0.1.1526532315
Xcode: 10.0
XQuartz: 2.7.11 => /opt/X11

brew doctor

(reproduces the issue. This seemed to start after upgrading to XCode 10.0, but I also regularly update homebrew)

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:
  pyqt-qt4
  isl@0.11
  numpy
  mpfr@2
  qt@5.7
  sip-qt4
  qscintilla2-qt4
/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:44: [BUG] Segmentation fault at 0x0000000000000000
ruby 2.3.7p456 (2018-03-28 revision 63024) [universal.x86_64-darwin9.0]

-- Crash Report log information --------------------------------------------
   See Crash Report log file under the one of following:
     * ~/Library/Logs/CrashReporter
     * /Library/Logs/CrashReporter
     * ~/Library/Logs/DiagnosticReports
     * /Library/Logs/DiagnosticReports
   for more details.
Don't forget to include the above Crash Report log file in bug reports.

-- Control frame information -----------------------------------------------
c:0020 p:0052 s:0112 e:000109 METHOD /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:44
c:0019 p:0278 s:0105 e:000104 METHOD /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:380
c:0018 p:0053 s:0091 e:000089 METHOD /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:350
c:0017 p:0089 s:0086 e:000085 METHOD /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:416
c:0016 p:0021 s:0081 e:000080 METHOD /usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:266
c:0015 p:0031 s:0078 e:000077 METHOD /usr/local/Homebrew/Library/Homebrew/keg.rb:197 [FINISH]
c:0014 p:---- s:0074 e:000073 CFUNC  :new
c:0013 p:0035 s:0070 e:000069 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1539
c:0012 p:0018 s:0067 e:000066 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1550
c:0011 p:0012 s:0059 e:000058 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1568
c:0010 p:0022 s:0053 e:000052 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1584
c:0009 p:0011 s:0048 e:000047 BLOCK  /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13 [FINISH]
c:0008 p:---- s:0044 e:000043 CFUNC  :each
c:0007 p:0019 s:0041 e:000040 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12
c:0006 p:0060 s:0035 e:000034 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652
c:0005 p:0085 s:0031 e:000030 BLOCK  /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46 [FINISH]
c:0004 p:---- s:0027 e:000026 CFUNC  :each
c:0003 p:0167 s:0024 e:000023 METHOD /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38
c:0002 p:0704 s:0017 E:002358 EVAL   /usr/local/Homebrew/Library/Homebrew/brew.rb:91 [FINISH]
c:0001 p:0000 s:0002 E:001630 (none) [FINISH]

-- Ruby level backtrace information ----------------------------------------
/usr/local/Homebrew/Library/Homebrew/brew.rb:91:in `<main>'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:in `doctor'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:in `each'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46:in `block in doctor'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652:in `check_missing_deps'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:in `missing_deps'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:in `each'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13:in `block in missing_deps'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1584:in `missing_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1568:in `runtime_formula_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1550:in `runtime_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1539:in `opt_or_installed_prefix_keg'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1539:in `new'
/usr/local/Homebrew/Library/Homebrew/keg.rb:197:in `initialize'
/usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:266:in `resolved_path'
/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:416:in `join'
/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:350:in `+'
/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:380:in `plus'
/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/pathname.rb:44:in `chop_basename'

-- Machine register context ------------------------------------------------
 rax: 0x0000000102001200 rbx: 0x0000000100f04da8 rcx: 0x0000000100c06ca0
 rdx: 0x62696c2f62696c2f rdi: 0x00000001020c50a0 rsi: 0x0000000000002007
 rbp: 0x00007ffeefbfd0d0 rsp: 0x00007ffeefbfd0d0  r8: 0x0000000000000004
  r9: 0x0000000000000006 r10: 0x00000001022b8830 r11: 0xfffffffffffffee8
 r12: 0x0000000000000002 r13: 0x0000000100d00370 r14: 0x0000000100f04de0
 r15: 0x0000000100dffb00 rip: 0x0000000100121612 rfl: 0x0000000000010202

-- Other runtime information -----------------------------------------------

* Loaded script: /usr/local/Homebrew/Library/Homebrew/brew.rb

* Loaded features:

    0 enumerator.so
    1 thread.rb
    2 rational.so
    3 complex.so
    4 encdb.so
    5 trans/transdb.so
    6 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/unicode_normalize.rb
    7 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/universal-darwin9.0/rbconfig.rb
    8 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/compatibility.rb
    9 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/defaults.rb
   10 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/deprecate.rb
   11 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/errors.rb
   12 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/version.rb
   13 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/requirement.rb
   14 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/platform.rb
   15 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/basic_specification.rb
   16 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/stub_specification.rb
   17 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/util/list.rb
   18 stringio.so
   19 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/rfc2396_parser.rb
   20 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/rfc3986_parser.rb
   21 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/common.rb
   22 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/generic.rb
   23 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/ftp.rb
   24 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/http.rb
   25 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/https.rb
   26 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/ldap.rb
   27 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/ldaps.rb
   28 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri/mailto.rb
   29 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/uri.rb
   30 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/specification.rb
   31 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/exceptions.rb
   32 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/dependency.rb
   33 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/core_ext/kernel_gem.rb
   34 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/monitor.rb
   35 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb
   36 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems.rb
   37 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/rubygems/path_support.rb
   38 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/version.rb
   39 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/core_ext/name_error.rb
   40 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/levenshtein.rb
   41 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/jaro_winkler.rb
   42 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkable.rb
   43 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/delegate.rb
   44 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkers/name_error_checkers/class_name_checker.rb
   45 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkers/name_error_checkers/variable_name_checker.rb
   46 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkers/name_error_checkers.rb
   47 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkers/method_name_checker.rb
   48 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/spell_checkers/null_checker.rb
   49 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean/formatter.rb
   50 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/gems/2.3.0/gems/did_you_mean-1.0.0/lib/did_you_mean.rb
   51 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/English.rb
   52 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/json/version.rb
   53 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/ostruct.rb
   54 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/json/generic_object.rb
   55 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/json/common.rb
   56 enc/utf_16be.so
   57 enc/utf_16le.so
   58 enc/utf_32be.so
   59 enc/utf_32le.so
   60 json/ext/parser.so
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   62 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/json/ext.rb
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  295 /usr/local/Homebrew/Library/Homebrew/formulary.rb
  296 /usr/local/Homebrew/Library/Homebrew/dependable.rb
  297 /usr/local/Homebrew/Library/Homebrew/dependency.rb
  298 /usr/local/Homebrew/Library/Homebrew/dependencies.rb
  299 /usr/local/Homebrew/Library/Homebrew/requirement.rb
  300 /usr/local/Homebrew/Library/Homebrew/requirements/linux_requirement.rb
  301 /usr/local/Homebrew/Library/Homebrew/requirements/macos_requirement.rb
  302 /usr/local/Homebrew/Library/Homebrew/requirements/maximum_macos_requirement.rb
  303 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/requirements/osxfuse_requirement.rb
  304 /usr/local/Homebrew/Library/Homebrew/extend/os/requirements/osxfuse_requirement.rb
  305 /usr/local/Homebrew/Library/Homebrew/requirements/osxfuse_requirement.rb
  306 /usr/local/Homebrew/Library/Homebrew/language/java.rb
  307 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/requirements/java_requirement.rb
  308 /usr/local/Homebrew/Library/Homebrew/extend/os/requirements/java_requirement.rb
  309 /usr/local/Homebrew/Library/Homebrew/requirements/java_requirement.rb
  310 /usr/local/Homebrew/Library/Homebrew/requirements/tuntap_requirement.rb
  311 /usr/local/Homebrew/Library/Homebrew/requirements/unsigned_kext_requirement.rb
  312 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/requirements/x11_requirement.rb
  313 /usr/local/Homebrew/Library/Homebrew/extend/os/requirements/x11_requirement.rb
  314 /usr/local/Homebrew/Library/Homebrew/requirements/x11_requirement.rb
  315 /usr/local/Homebrew/Library/Homebrew/requirements/arch_requirement.rb
  316 /usr/local/Homebrew/Library/Homebrew/requirements/xcode_requirement.rb
  317 /usr/local/Homebrew/Library/Homebrew/requirements.rb
  318 /usr/local/Homebrew/Library/Homebrew/os/mac/ld64_dependency.rb
  319 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/dependency_collector.rb
  320 /usr/local/Homebrew/Library/Homebrew/extend/os/dependency_collector.rb
  321 /usr/local/Homebrew/Library/Homebrew/dependency_collector.rb
  322 /usr/local/Homebrew/Library/Homebrew/patch.rb
  323 /usr/local/Homebrew/Library/Homebrew/extend/os/software_spec.rb
  324 /usr/local/Homebrew/Library/Homebrew/software_spec.rb
  325 /usr/local/Homebrew/Library/Homebrew/install_renamed.rb
  326 /usr/local/Homebrew/Library/Homebrew/pkg_version.rb
  327 /usr/local/Homebrew/Library/Homebrew/migrator.rb
  328 /usr/local/Homebrew/Library/Homebrew/linkage_cache_store.rb
  329 /usr/local/Homebrew/Library/Homebrew/extend/os/linkage_checker.rb
  330 /usr/local/Homebrew/Library/Homebrew/linkage_checker.rb
  331 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/extend/ENV/shared.rb
  332 /usr/local/Homebrew/Library/Homebrew/extend/os/extend/ENV/shared.rb
  333 /usr/local/Homebrew/Library/Homebrew/extend/ENV/shared.rb
  334 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/extend/ENV/std.rb
  335 /usr/local/Homebrew/Library/Homebrew/extend/os/extend/ENV/std.rb
  336 /usr/local/Homebrew/Library/Homebrew/extend/ENV/std.rb
  337 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/extend/ENV/super.rb
  338 /usr/local/Homebrew/Library/Homebrew/extend/os/extend/ENV/super.rb
  339 /usr/local/Homebrew/Library/Homebrew/extend/ENV/super.rb
  340 /usr/local/Homebrew/Library/Homebrew/extend/ENV.rb
  341 /usr/local/Homebrew/Library/Homebrew/formula.rb
  342 /usr/local/Homebrew/Library/Homebrew/readall.rb
  343 /usr/local/Homebrew/Library/Homebrew/tap.rb
  344 /usr/local/Homebrew/Library/Homebrew/compat/os/mac.rb
  345 /usr/local/Homebrew/Library/Homebrew/compat/dependable.rb
  346 /usr/local/Homebrew/Library/Homebrew/compat/dependency_collector.rb
  347 /usr/local/Homebrew/Library/Homebrew/compat/fileutils.rb
  348 /usr/local/Homebrew/Library/Homebrew/compat/formula_support.rb
  349 /usr/local/Homebrew/Library/Homebrew/compat/cask/cask_loader.rb
  350 /usr/local/Homebrew/Library/Homebrew/cask/cmd/options.rb
  351 /usr/local/Homebrew/Library/Homebrew/searchable.rb
  352 /usr/local/Homebrew/Library/Homebrew/cask/cask_loader.rb
  353 /usr/local/Homebrew/Library/Homebrew/cask/config.rb
  354 /usr/local/Homebrew/Library/Homebrew/locale.rb
  355 /usr/local/Homebrew/Library/Homebrew/cask/artifact/abstract_artifact.rb
  356 /usr/local/Homebrew/Library/Homebrew/cask/artifact/relocated.rb
  357 /usr/local/Homebrew/Library/Homebrew/cask/artifact/moved.rb
  358 /usr/local/Homebrew/Library/Homebrew/cask/artifact/app.rb
  359 /usr/local/Homebrew/Library/Homebrew/cask/artifact/artifact.rb
  360 /usr/local/Homebrew/Library/Homebrew/cask/artifact/symlinked.rb
  361 /usr/local/Homebrew/Library/Homebrew/cask/artifact/binary.rb
  362 /usr/local/Homebrew/Library/Homebrew/cask/artifact/colorpicker.rb
  363 /usr/local/Homebrew/Library/Homebrew/cask/artifact/dictionary.rb
  364 /usr/local/Homebrew/Library/Homebrew/cask/artifact/font.rb
  365 /usr/local/Homebrew/Library/Homebrew/cask/artifact/input_method.rb
  366 /usr/local/Homebrew/Library/Homebrew/cask/artifact/installer.rb
  367 /usr/local/Homebrew/Library/Homebrew/cask/artifact/internet_plugin.rb
  368 /usr/local/Homebrew/Library/Homebrew/cask/artifact/audio_unit_plugin.rb
  369 /usr/local/Homebrew/Library/Homebrew/cask/artifact/vst_plugin.rb
  370 /usr/local/Homebrew/Library/Homebrew/cask/artifact/vst3_plugin.rb
  371 /usr/local/Homebrew/Library/Homebrew/cask/artifact/pkg.rb
  372 /usr/local/Homebrew/Library/Homebrew/cask/artifact/abstract_flight_block.rb
  373 /usr/local/Homebrew/Library/Homebrew/cask/artifact/postflight_block.rb
  374 /usr/local/Homebrew/Library/Homebrew/cask/artifact/preflight_block.rb
  375 /usr/local/Homebrew/Library/Homebrew/cask/artifact/prefpane.rb
  376 /usr/local/Homebrew/Library/Homebrew/cask/artifact/qlplugin.rb
  377 /usr/local/Homebrew/Library/Homebrew/cask/artifact/screen_saver.rb
  378 /usr/local/Homebrew/Library/Homebrew/cask/artifact/service.rb
  379 /usr/local/Homebrew/Library/Homebrew/cask/artifact/stage_only.rb
  380 /usr/local/Homebrew/Library/Homebrew/cask/artifact/suite.rb
  381 /usr/local/Homebrew/Library/Homebrew/cask/artifact/abstract_uninstall.rb
  382 /usr/local/Homebrew/Library/Homebrew/cask/artifact/uninstall.rb
  383 /usr/local/Homebrew/Library/Homebrew/cask/artifact/zap.rb
  384 /usr/local/Homebrew/Library/Homebrew/cask/artifact.rb
  385 /usr/local/Homebrew/Library/Homebrew/cask/caskroom.rb
  386 /usr/local/Homebrew/Library/Homebrew/cask/exceptions.rb
  387 /usr/local/Homebrew/Library/Homebrew/cask/dsl/appcast.rb
  388 /usr/local/Homebrew/Library/Homebrew/cask/dsl/base.rb
  389 /usr/local/Homebrew/Library/Homebrew/cask/dsl/caveats.rb
  390 /usr/local/Homebrew/Library/Homebrew/cask/dsl/conflicts_with.rb
  391 /usr/local/Homebrew/Library/Homebrew/cask/dsl/container.rb
  392 /usr/local/Homebrew/Library/Homebrew/cask/dsl/depends_on.rb
  393 /usr/local/Homebrew/Library/Homebrew/cask/staged.rb
  394 /usr/local/Homebrew/Library/Homebrew/cask/dsl/postflight.rb
  395 /usr/local/Homebrew/Library/Homebrew/cask/dsl/preflight.rb
  396 /usr/local/Homebrew/Library/Homebrew/cask/dsl/uninstall_postflight.rb
  397 /usr/local/Homebrew/Library/Homebrew/cask/dsl/uninstall_preflight.rb
  398 /usr/local/Homebrew/Library/Homebrew/cask/dsl/version.rb
  399 /usr/local/Homebrew/Library/Homebrew/cask/url.rb
  400 /usr/local/Homebrew/Library/Homebrew/cask/dsl.rb
  401 /usr/local/Homebrew/Library/Homebrew/cask/metadata.rb
  402 /usr/local/Homebrew/Library/Homebrew/cask/cask.rb
  403 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/search.rb
  404 /usr/local/Homebrew/Library/Homebrew/extend/os/search.rb
  405 /usr/local/Homebrew/Library/Homebrew/search.rb
  406 /usr/local/Homebrew/Library/Homebrew/cask/cmd/abstract_command.rb
  407 /usr/local/Homebrew/Library/Homebrew/cmd/--version.rb
  408 /usr/local/Homebrew/Library/Homebrew/compat/cask/cmd/--version.rb
  409 /usr/local/Homebrew/Library/Homebrew/cleanup.rb
  410 /usr/local/Homebrew/Library/Homebrew/compat/cask/cmd/cleanup.rb
  411 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/missing_formula.rb
  412 /usr/local/Homebrew/Library/Homebrew/extend/os/missing_formula.rb
  413 /usr/local/Homebrew/Library/Homebrew/missing_formula.rb
  414 /usr/local/Homebrew/Library/Homebrew/formula_versions.rb
  415 /usr/local/Homebrew/Library/Homebrew/descriptions.rb
  416 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/optparse.rb
  417 /usr/local/Homebrew/Library/Homebrew/cli_parser.rb
  418 /usr/local/Homebrew/Library/Homebrew/cmd/search.rb
  419 /usr/local/Homebrew/Library/Homebrew/compat/cask/cmd/search.rb
  420 /usr/local/Homebrew/Library/Homebrew/compat/cask/cache.rb
  421 /usr/local/Homebrew/Library/Homebrew/compat/cask/caskroom.rb
  422 /usr/local/Homebrew/Library/Homebrew/compat/cask/dsl.rb
  423 /usr/local/Homebrew/Library/Homebrew/compat/cask.rb
  424 /usr/local/Homebrew/Library/Homebrew/compat/tap.rb
  425 /usr/local/Homebrew/Library/Homebrew/compat.rb
  426 /usr/local/Homebrew/Library/Homebrew/global.rb
  427 /usr/local/Homebrew/Library/Homebrew/cask/cache.rb
  428 /usr/local/Homebrew/Library/Homebrew/cask/quarantine.rb
  429 /usr/local/Homebrew/Library/Homebrew/cask/verify.rb
  430 /usr/local/Homebrew/Library/Homebrew/cask/download.rb
  431 /usr/local/Homebrew/Library/Homebrew/update_migrator.rb
  432 /usr/local/Homebrew/Library/Homebrew/extend/os/mac/diagnostic.rb
  433 /usr/local/Homebrew/Library/Homebrew/extend/os/diagnostic.rb
  434 /usr/local/Homebrew/Library/Homebrew/diagnostic.rb
  435 /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb
  436 /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/lib/ruby/2.3.0/find.rb
  437 /usr/local/Homebrew/Library/Taps/osgeo/homebrew-osgeo4mac/Requirements/qgis_requirements.rb

[NOTE]
You may have encountered a bug in the Ruby interpreter or extension libraries.
Bug reports are welcome.
For details: http://www.ruby-lang.org/bugreport.html

Abort trap: 6
MikeMcQuaid commented 6 years ago

@ansonhoyt Please try to rm -rf /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby.

ansonhoyt commented 6 years ago

Thanks! Tried and it still fails...

$ rm -rf /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby
$ brew update
Already up-to-date.
$ brew doctor

brew config

The "Homebrew ruby" changed

HOMEBREW_VERSION: 1.7.6-9-g2ea3aee
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 2ea3aee461f4b2f22ccc9b6f72b4426448bc1039
Last commit: 5 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7a8d0b66d5e62ba80d3f545083b850306b17c57e
Core tap last commit: 36 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.19.0 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.2, 1.8.0_72, 1.6.0_33-b03-424, 1.6.0_29-b11-402
macOS: 10.13.6-x86_64
CLT: 9.4.0.0.1.1526532315
Xcode: 10.0
XQuartz: 2.7.11 => /opt/X11

brew doctor

Stack trace looks slightly different.

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:
  pyqt-qt4
  isl@0.11
  numpy
  mpfr@2
  qt@5.7
  sip-qt4
  qscintilla2-qt4
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:44: [BUG] Segmentation fault at 0x0000000000000000
ruby 2.3.7p456 (2018-03-28 revision 63024) [universal.x86_64-darwin17]

-- Crash Report log information --------------------------------------------
   See Crash Report log file under the one of following:
     * ~/Library/Logs/CrashReporter
     * /Library/Logs/CrashReporter
     * ~/Library/Logs/DiagnosticReports
     * /Library/Logs/DiagnosticReports
   for more details.
Don't forget to include the above Crash Report log file in bug reports.

-- Control frame information -----------------------------------------------
c:0019 p:0055 s:0108 e:000107 METHOD /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:44
c:0018 p:0068 s:0103 e:000102 METHOD /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:358
c:0017 p:0053 s:0089 e:000087 METHOD /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:350
c:0016 p:0157 s:0084 e:000083 METHOD /usr/local/Homebrew/Library/Homebrew/keg.rb:204 [FINISH]
c:0015 p:---- s:0080 e:000079 CFUNC  :new
c:0014 p:0035 s:0076 e:000075 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1539
c:0013 p:0008 s:0073 e:000072 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1786
c:0012 p:0076 s:0068 e:000066 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1562
c:0011 p:0012 s:0059 e:000058 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1568
c:0010 p:0022 s:0053 e:000052 METHOD /usr/local/Homebrew/Library/Homebrew/formula.rb:1584
c:0009 p:0011 s:0048 e:000047 BLOCK  /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13 [FINISH]
c:0008 p:---- s:0044 e:000043 CFUNC  :each
c:0007 p:0019 s:0041 e:000040 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12
c:0006 p:0060 s:0035 e:000034 METHOD /usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652
c:0005 p:0085 s:0031 e:000030 BLOCK  /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46 [FINISH]
c:0004 p:---- s:0027 e:000026 CFUNC  :each
c:0003 p:0167 s:0024 e:000023 METHOD /usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38
c:0002 p:0704 s:0017 E:000a08 EVAL   /usr/local/Homebrew/Library/Homebrew/brew.rb:91 [FINISH]
c:0001 p:0000 s:0002 E:000f60 (none) [FINISH]

-- Ruby level backtrace information ----------------------------------------
/usr/local/Homebrew/Library/Homebrew/brew.rb:91:in `<main>'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:in `doctor'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:38:in `each'
/usr/local/Homebrew/Library/Homebrew/cmd/doctor.rb:46:in `block in doctor'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:652:in `check_missing_deps'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:in `missing_deps'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:12:in `each'
/usr/local/Homebrew/Library/Homebrew/diagnostic.rb:13:in `block in missing_deps'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1584:in `missing_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1568:in `runtime_formula_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1562:in `runtime_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1786:in `undeclared_runtime_dependencies'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1539:in `opt_or_installed_prefix_keg'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1539:in `new'
/usr/local/Homebrew/Library/Homebrew/keg.rb:204:in `initialize'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:350:in `+'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:358:in `plus'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/pathname.rb:44:in `chop_basename'

-- Machine register context ------------------------------------------------
 rax: 0x6173776f632f7261 rbx: 0x00007f9d1bb18108 rcx: 0x0000000000000000
 rdx: 0x0000000000000000 rdi: 0x000034302e332f79 rsi: 0x00007f9d1bb18108
 rbp: 0x00007ffeea9e96e0 rsp: 0x00007ffeea9e96a0  r8: 0x00007f9d1bb1bc90
  r9: 0x0000000000000000 r10: 0x00007f9d1b800410 r11: 0x0000000000000000
 r12: 0x00007f9d1bb18000 r13: 0x00007f9d1e7898f0 r14: 0x00007f9d1a500a80
 r15: 0x0000000000000000 rip: 0x00007fff38e7a1df rfl: 0x0000000000010202

-- C level backtrace information -------------------------------------------
0   Ruby                                0x00007fff38f5f080 rb_print_backtrace + 29
1   Ruby                                0x00007fff38f5f257 rb_vm_bugreport + 364
2   Ruby                                0x00007fff38e5b400 rb_bug_context + 206
3   Ruby                                0x00007fff38ef735a Init_signal + 3242
4   libsystem_platform.dylib            0x00007fff5596df5a _sigtramp + 26
5   Ruby                                0x00007fff38e7a1df Init_GC + 18199
6   Ruby                                0x00007fff38e729f9 rb_gc + 154
7   Ruby                                0x00007fff38e70f47 rb_gc_finalize_deferred + 159
8   Ruby                                0x00007fff38f632b7 rb_postponed_job_flush + 242
9   Ruby                                0x00007fff38f65987 rb_threadptr_execute_interrupts + 74
10  Ruby                                0x00007fff38f4969c rb_vm_get_insns_address_table + 8788
11  Ruby                                0x00007fff38f53c05 rb_iseq_eval + 412
12  Ruby                                0x00007fff38f5c9cb rb_vm_fstring_table + 26422
13  Ruby                                0x00007fff38f4e8b1 rb_funcallv + 224
14  Ruby                                0x00007fff38ea45cb rb_class_new_instance + 41
15  Ruby                                0x00007fff38f5779a rb_vm_fstring_table + 5381
16  Ruby                                0x00007fff38f49006 rb_vm_get_insns_address_table + 7102
17  Ruby                                0x00007fff38f53c05 rb_iseq_eval + 412
18  Ruby                                0x00007fff38f50e65 rb_yield_1 + 75
19  Ruby                                0x00007fff38e2e40a rb_ary_each + 51
20  Ruby                                0x00007fff38f5779a rb_vm_fstring_table + 5381
21  Ruby                                0x00007fff38f48f30 rb_vm_get_insns_address_table + 6888
22  Ruby                                0x00007fff38f53c05 rb_iseq_eval + 412
23  Ruby                                0x00007fff38f50e65 rb_yield_1 + 75
24  Ruby                                0x00007fff38e2e40a rb_ary_each + 51
25  Ruby                                0x00007fff38f5779a rb_vm_fstring_table + 5381
26  Ruby                                0x00007fff38f48f30 rb_vm_get_insns_address_table + 6888
27  Ruby                                0x00007fff38f53c05 rb_iseq_eval + 412
28  Ruby                                0x00007fff38e5fe92 ruby_exec_node + 232
29  Ruby                                0x00007fff38e5fd85 ruby_run_node + 39
30  ruby                                0x00000001052151bd main + 98

-- Other runtime information -----------------------------------------------

* Loaded script: /usr/local/Homebrew/Library/Homebrew/brew.rb

* Loaded features:

    0 enumerator.so
    1 thread.rb
    2 rational.so
    3 complex.so
    4 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin17/enc/encdb.bundle
    5 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin17/enc/trans/transdb.bundle
    6 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/unicode_normalize.rb
    7 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin17/rbconfig.rb
    8 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/compatibility.rb
    9 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/defaults.rb
   10 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/deprecate.rb
   11 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/errors.rb
   12 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/version.rb
   13 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/requirement.rb
   14 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/platform.rb
   15 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/basic_specification.rb
   16 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/stub_specification.rb
   17 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/util/list.rb
   18 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin17/stringio.bundle
   19 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/rfc2396_parser.rb
   20 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/rfc3986_parser.rb
   21 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/common.rb
   22 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/generic.rb
   23 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/ftp.rb
   24 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/http.rb
   25 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/https.rb
   26 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/ldap.rb
   27 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/ldaps.rb
   28 /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/uri/mailto.rb
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[NOTE]
You may have encountered a bug in the Ruby interpreter or extension libraries.
Bug reports are welcome.
For details: http://www.ruby-lang.org/bugreport.html

Abort trap: 6
MikeMcQuaid commented 6 years ago

@ansonhoyt there's nothing we can do about that I'm afraid; it seems to be an issue with your system Ruby installation. You may need to remove any gems you have installed for it.

ansonhoyt commented 6 years ago

I uninstalled all possible gems from my system ruby:

$ rvm use system
$ gem clean
$ gem uninstall <I tried each gem in `gem list`>

I think this leaves me with just gems that can't (and shouldn't) be removed:

$ gem list

*** LOCAL GEMS ***

bigdecimal (1.2.8)
CFPropertyList (2.2.8)
did_you_mean (1.0.0)
io-console (0.4.5)
json (1.8.3.1)
libxml-ruby (2.9.0)
minitest (5.8.5)
net-telnet (0.1.1)
nokogiri (1.5.6)
power_assert (0.2.6)
psych (2.1.0.1)
rake (10.4.2)
rdoc (4.2.1)
sqlite3 (1.3.11)
test-unit (3.1.5)

$ gem uninstall bigdecimal
ERROR:  While executing gem ... (Gem::InstallError)
    gem "bigdecimal" cannot be uninstalled because it is a default gem

Now brew doctor still fails on check_missing_deps, but now on CacheStoreDatabase.set. I output the key/value parameters and saw it fails when setting a big value for qt:

# puts statement in CacheStoreDatabase.set
key = "/usr/local/Cellar/cowsay/3.04"
key = "/usr/local/Cellar/ossp-uuid/1.6.2_2"
key = "/usr/local/Cellar/pidof/0.1.4"
key = "/usr/local/Cellar/cscope/15.8b"
key = "/usr/local/Cellar/texi2html/5.0"
key = "/usr/local/Cellar/qt-4/4.8.7"

This is an older qt, since brew install qt wants to install qt 5.11.2. I get a similar stack trace when I try brew uninstall qt4 while it is checking the dependencies.

If I make CacheStoreDatabase.set into a no-op where it returns immediately, then brew doctor succeeds and brew uninstall qt4 shows me the dependencies that need it.

So, It seems like there may be a Homebrew issue. However, I realize that can be hard to tell and you're much more experienced at that assessment than I 😄

ansonhoyt commented 6 years ago

In CacheStoreDatabase.set(key, value) the statement db[key] = value fails for:

key:

/usr/local/Cellar/qt-4/4.8.7

value:

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ansonhoyt commented 6 years ago

Seemed that making set a no-op and re-installing each failing package allowed it to progress down the list.

Looking for a way to clear the whole cache, I found CacheStoreDatabase.cache_path and deleted the file: rm /Users/ahoyt/Library/Caches/Homebrew/linkage.db.

Now brew doctor works:

$ 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:
  isl@0.11
  numpy
  mpfr@2
  qt@5.7
  sip-qt4

Clearing the cache file seemed to fix things up!

MikeMcQuaid commented 6 years ago

Need to figure out why https://github.com/Homebrew/brew/blob/d4f8335f0a73803e628ba2636d1d2f3a00930202/Library/Homebrew/cache_store.rb#L74-L99 is not successful for you.

MikeMcQuaid commented 6 years ago

@ansonhoyt Please brew update and see if you can reproduce this.

ansonhoyt commented 6 years ago

Hope to give it a try tomorrow. I'll see if I can restore linkage.db from Time Machine to reproduce, then update to see if it resolves.

MikeMcQuaid commented 6 years ago

Great, thanks.

ansonhoyt commented 6 years ago

Restoring linkage.db didn't reproduce the issue, brew doctor was fine. I noticed my homebrew version was 1.7.6-11-gd4f8335, so I also tried with my previous brew revision.

$ cd /usr/local/Homebrew/Library
$ git checkout 2ea3aee461f4b2f22ccc9b6f72b4426448bc1039
$ brew config
$ brew doctor

After I checked out my earlier revision and got a segfault, but it looked different. Also, I couldn't get it to happen again. I tried repeating the linkage.db restore and still working fine.

Here's my one-off stack trace in case it is useful: https://gist.github.com/ansonhoyt/5cacbfa9ede36c9e11daa599cb46f643

Also, brew doctor has no errors after updating to 1.7.6-20-gbb177b3.

Sorry I wasn't able to give a better test.

MikeMcQuaid commented 6 years ago

@ansonhoyt That you can't reproduce it any more is good, thanks 👍