Homebrew-core: Percona Toolkit: pt-schema-online-change crashes with SIGSEGV (macOS 10.15.2)

[nTraum]

• [x] ran brew update and can still reproduce the problem?
• [x] ran brew doctor, fixed all issues and can still reproduce the problem?
• [x] ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
• [x] if brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?

brew config
HOMEBREW_VERSION: 2.2.2-52-g40765b4
ORIGIN: https://github.com/Homebrew/brew
HEAD: 40765b4a723afe38ac5aae23bad6973ae89ceb6b
Last commit: 13 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 23405a3a7c39f1fad936afe54d259de27f748cfe
Core tap last commit: 22 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_BREW_GIT_REMOTE: https://github.com/Homebrew/brew
HOMEBREW_CORE_GIT_REMOTE: https://github.com/Homebrew/homebrew-core
HOMEBREW_DEV_CMD_RUN: 1
CPU: octa-core 64-bit kabylake
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
Clang: 11.0 build 1100
Git: 2.24.1 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 10.15.2-x86_64
CLT: 11.3.0.0.1.1574140115
Xcode: 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 or file an issue; just ignore this. Thanks!

Warning: You have installed Bitdefender. The "Traffic Scan" option interferes with
Homebrew's ability to download packages. See:
  https://github.com/Homebrew/brew/issues/5558

What you were trying to do (and why)

I'd like to run the executable pt-schema-online-change, as provided by the percona-toolkit formula.

What happened (include command output)

When running the command, it aborts with SIGSEGV.

Command output

fish: 'pt-online-schema-change --help' terminated by signal SIGSEGV (Address boundary error)

What you expected to happen

I expected the executable to not crash with SIGSEGV, but print the help instead.

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

brew install percona-toolkit
pt-online-schema-change --help

Thanks in advance for looking into this, please let me know if I can help with further information.

[bayandin]

Looks like it's a perl from homebrew is crashing in this script (I've tried both the latest 5.30.1 and the previous one 5.30.0)

the crash

Process:               perl [57241]
Path:                  /usr/local/Cellar/perl/5.30.1/bin/perl
Identifier:            perl
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        bash [45442]
Responsible:           Terminal [26163]
User ID:               501

Date/Time:             2020-01-06 11:29:14.405 +0000
OS Version:            Mac OS X 10.15.2 (19C57)
Report Version:        12
Bridge OS Version:     4.2 (17P2551)
Anonymous UUID:        DDB8645B-2B74-EA51-E23D-3548F0CAD381

Sleep/Wake UUID:       4E105A6E-D28F-4C46-BE51-A5D4B862697A

Time Awake Since Boot: 110000 seconds
Time Since Wake:       1500 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000005
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [57241]

VM Regions Near 0x5:
--> 
    __TEXT                 000000010d389000-000000010d38b000 [    8K] r-x/r-x SM=COW  /usr/local/Cellar/perl/5.30.1/bin/perl

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   DBI.bundle                      0x000000010d71b7d0 boot_DBI + 32
1   libperl.dylib                   0x000000010d43ba98 Perl_pp_entersub + 1337
2   libperl.dylib                   0x000000010d432143 Perl_runops_standard + 19
3   libperl.dylib                   0x000000010d3b1d58 Perl_call_sv + 870
4   libperl.dylib                   0x000000010d3aeb92 Perl_call_list + 399
5   libperl.dylib                   0x000000010d3a265f S_process_special_blocks + 428
6   libperl.dylib                   0x000000010d39bf4d Perl_newATTRSUB_x + 4695
7   libperl.dylib                   0x000000010d3ddfb4 Perl_yyparse + 4828
8   libperl.dylib                   0x000000010d475b09 S_doeval_compile + 1405
9   libperl.dylib                   0x000000010d47436b Perl_pp_require + 5042
10  libperl.dylib                   0x000000010d432143 Perl_runops_standard + 19
11  libperl.dylib                   0x000000010d3b16b4 S_run_body + 124
12  libperl.dylib                   0x000000010d3b14c0 perl_run + 322
13  perl                            0x000000010d38ae02 main + 182
14  libdyld.dylib                   0x00007fff71cda7fd start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000005  rbx: 0x0000000000000001  rcx: 0x0000000000000001  rdx: 0x0000000000000009
  rdi: 0x00007fced7800600  rsi: 0x00007fcee0526800  rbp: 0x00007ffee2875b60  rsp: 0x00007ffee2875b20
   r8: 0x0000000000000002   r9: 0x0000000000000001  r10: 0x00000000f81fffff  r11: 0xffffffffffff7cf0
  r12: 0x0000000000000000  r13: 0x00007fced7800600  r14: 0x00007fced7800600  r15: 0x00007ffee2875c70
  rip: 0x000000010d71b7d0  rfl: 0x0000000000010202  cr2: 0x0000000000000005

Logical CPU:     2
Error Code:      0x00000004 (no mapping for user data write)
Trap Number:     14


Binary Images:
       0x10d389000 -        0x10d38afff +perl (0) <5C92A5E8-8860-37A2-A27D-A27F4957A956> /usr/local/bin/perl
       0x10d38e000 -        0x10d626ff3 +libperl.dylib (0) <119CE414-6A79-3B72-B22D-C0160189406E> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/CORE/libperl.dylib
       0x10d693000 -        0x10d694fff +NamedCapture.bundle (0)  /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Tie/Hash/NamedCapture/NamedCapture.bundle
       0x10d698000 -        0x10d69effb +Dumper.bundle (0)  /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Data/Dumper/Dumper.bundle
       0x10d6a3000 -        0x10d6abffb +Util.bundle (0) <070320C9-2511-310B-B00E-535B0ACED8AD> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/List/Util/Util.bundle
       0x10d6b0000 -        0x10d6b2fff +mro.bundle (0) <1586C16A-C576-3D76-A17C-7364956CF57B> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/mro/mro.bundle
       0x10d6b7000 -        0x10d6b8fff +Fcntl.bundle (0) <756FB4A4-12BE-3071-9357-3765E9208CF5> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Fcntl/Fcntl.bundle
       0x10d6bc000 -        0x10d6c9ff7 +POSIX.bundle (0)  /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/POSIX/POSIX.bundle
       0x10d6d2000 -        0x10d6d6fff +HiRes.bundle (0)  /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Time/HiRes/HiRes.bundle
       0x10d6dc000 -        0x10d6deff7 +MD5.bundle (0) <77D02F56-638C-30C9-B455-02E203D80B1F> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Digest/MD5/MD5.bundle
       0x10d6e2000 -        0x10d6eefff +B.bundle (0) <51BBD2D4-2398-34AD-B73B-00B694CBB218> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/B/B.bundle
       0x10d6f6000 -        0x10d6f8fff +IO.bundle (0) <9CCD31FE-1D3A-32DD-BFD4-94E3BA45498C> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/IO/IO.bundle
       0x10d6fd000 -        0x10d702fff +Socket.bundle (0) <939AFD4D-BFB4-3075-85BD-E7A5E470DC61> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Socket/Socket.bundle
       0x10d708000 -        0x10d708fff +Hostname.bundle (0)  /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Sys/Hostname/Hostname.bundle
       0x10d70c000 -        0x10d70eff7 +Cwd.bundle (0) <5EC9B363-7B6B-3296-9FDC-9FE5CA521DBA> /usr/local/Cellar/perl/5.30.1/lib/perl5/5.30.1/darwin-thread-multi-2level/auto/Cwd/Cwd.bundle
       0x10d712000 -        0x10d72aff7 +DBI.bundle (0) <05226907-77ED-3784-9BBF-5CA61AE5A7C1> /usr/local/Cellar/percona-toolkit/3.0.13_2/libexec/lib/perl5/darwin-thread-multi-2level/auto/DBI/DBI.bundle
       0x11632e000 -        0x1163becb7  dyld (733.8)  /usr/lib/dyld
    0x7fff6eb09000 -     0x7fff6eb0aff3  libSystem.B.dylib (1281) <2F6BCFD9-A5F9-30FE-BF5A-5C53D3CBAB4D> /usr/lib/libSystem.B.dylib
    0x7fff6edef000 -     0x7fff6ee42ff7  libc++.1.dylib (800.7) <6018A70E-5CD3-32AF-BA60-E7A0B7E7CEB2> /usr/lib/libc++.1.dylib
    0x7fff6ee43000 -     0x7fff6ee57fff  libc++abi.dylib (800.7)  /usr/lib/libc++abi.dylib
    0x7fff7095a000 -     0x7fff7098bfc6  libobjc.A.dylib (781.2) <17241F77-6A7A-39D7-8836-63E2725AA3C9> /usr/lib/libobjc.A.dylib
    0x7fff70f10000 -     0x7fff70f13ffb  libutil.dylib (57) <86C9C769-0523-38C6-940E-900C8CAB780A> /usr/lib/libutil.dylib
    0x7fff71aac000 -     0x7fff71ab1ff3  libcache.dylib (83)  /usr/lib/system/libcache.dylib
    0x7fff71ab2000 -     0x7fff71abdfff  libcommonCrypto.dylib (60165)  /usr/lib/system/libcommonCrypto.dylib
    0x7fff71abe000 -     0x7fff71ac5fff  libcompiler_rt.dylib (101.2) <51107CAA-0727-370D-8287-940D40D09AC1> /usr/lib/system/libcompiler_rt.dylib
    0x7fff71ac6000 -     0x7fff71acffff  libcopyfile.dylib (166.40.1) <6454A046-88E5-32D6-898C-FB0D30D28637> /usr/lib/system/libcopyfile.dylib
    0x7fff71ad0000 -     0x7fff71b67fe7  libcorecrypto.dylib (866.60.3) <8090C446-35C8-31B4-8B1E-AF6D0EF3524B> /usr/lib/system/libcorecrypto.dylib
    0x7fff71c7e000 -     0x7fff71cbfff0  libdispatch.dylib (1173.60.1)  /usr/lib/system/libdispatch.dylib
    0x7fff71cc0000 -     0x7fff71cf5ff7  libdyld.dylib (733.8) <8E2D3DED-0756-37A0-9D55-B9264CA020B4> /usr/lib/system/libdyld.dylib
    0x7fff71cf6000 -     0x7fff71cf6ffb  libkeymgr.dylib (30) <0B9A3AF7-086E-3E7A-A52E-3DAF2E52CF86> /usr/lib/system/libkeymgr.dylib
    0x7fff71d04000 -     0x7fff71d04ff7  liblaunch.dylib (1738.61.1)  /usr/lib/system/liblaunch.dylib
    0x7fff71d05000 -     0x7fff71d0aff7  libmacho.dylib (949.0.1) <9831715F-ED86-3A9D-88CD-152C888B784B> /usr/lib/system/libmacho.dylib
    0x7fff71d0b000 -     0x7fff71d0dff7  libquarantine.dylib (110.40.3) <58CE8913-EC7B-376B-BC80-69763993A1E4> /usr/lib/system/libquarantine.dylib
    0x7fff71d0e000 -     0x7fff71d0fff7  libremovefile.dylib (48) <4E1AD797-3993-3E05-BB9B-B4E3038CE09C> /usr/lib/system/libremovefile.dylib
    0x7fff71d10000 -     0x7fff71d27fff  libsystem_asl.dylib (377.60.2) <2CD6CABE-F8D7-3CCA-A930-08F8AC356D30> /usr/lib/system/libsystem_asl.dylib
    0x7fff71d28000 -     0x7fff71d28fff  libsystem_blocks.dylib (74) <71A75F21-83AD-382F-95E4-4D6B77B4B9FE> /usr/lib/system/libsystem_blocks.dylib
    0x7fff71d29000 -     0x7fff71db0ff7  libsystem_c.dylib (1353.60.8)  /usr/lib/system/libsystem_c.dylib
    0x7fff71db1000 -     0x7fff71db4ffb  libsystem_configuration.dylib (1061.40.2)  /usr/lib/system/libsystem_configuration.dylib
    0x7fff71db5000 -     0x7fff71db8ff7  libsystem_coreservices.dylib (114)  /usr/lib/system/libsystem_coreservices.dylib
    0x7fff71db9000 -     0x7fff71dc1fff  libsystem_darwin.dylib (1353.60.8) <9AC37996-630C-3B1E-8285-CFC77B684359> /usr/lib/system/libsystem_darwin.dylib
    0x7fff71dc2000 -     0x7fff71dc9ffb  libsystem_dnssd.dylib (1096.60.2) <7F0DF910-F4AC-3CED-9494-295B5E45549C> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff71dca000 -     0x7fff71dcbffb  libsystem_featureflags.dylib (17) <985005B7-C0B3-3DCA-B064-6D34A0687212> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff71dcc000 -     0x7fff71e19fff  libsystem_info.dylib (538)  /usr/lib/system/libsystem_info.dylib
    0x7fff71e1a000 -     0x7fff71e46ff7  libsystem_kernel.dylib (6153.61.1) <90F8650F-D3A9-38B3-BB8C-B5D3686393BC> /usr/lib/system/libsystem_kernel.dylib
    0x7fff71e47000 -     0x7fff71e8efcf  libsystem_m.dylib (3178) <92F1FF45-BD1C-32FE-A9A9-D12AF02C8212> /usr/lib/system/libsystem_m.dylib
    0x7fff71e8f000 -     0x7fff71eb6fff  libsystem_malloc.dylib (283.60.1) <51472F42-71BE-348F-B42E-4EDD3040B690> /usr/lib/system/libsystem_malloc.dylib
    0x7fff71eb7000 -     0x7fff71ec4ffb  libsystem_networkextension.dylib (1095.60.2) <846C06C0-A705-38AE-8A29-3FA4153252B3> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff71ec5000 -     0x7fff71eceff3  libsystem_notify.dylib (241) <7CB7DE46-5877-3CAD-8526-CACEA22F3AD5> /usr/lib/system/libsystem_notify.dylib
    0x7fff71ecf000 -     0x7fff71ed8fef  libsystem_platform.dylib (220)  /usr/lib/system/libsystem_platform.dylib
    0x7fff71ed9000 -     0x7fff71ee3fff  libsystem_pthread.dylib (416.60.2) <9D14694F-F3FE-385D-9B23-6A87844D5CBF> /usr/lib/system/libsystem_pthread.dylib
    0x7fff71ee4000 -     0x7fff71ee8fff  libsystem_sandbox.dylib (1217.61.1)  /usr/lib/system/libsystem_sandbox.dylib
    0x7fff71ee9000 -     0x7fff71eebfff  libsystem_secinit.dylib (62.60.1) <129C187A-E580-3F00-A0C3-E96A633364F1> /usr/lib/system/libsystem_secinit.dylib
    0x7fff71eec000 -     0x7fff71ef3ffb  libsystem_symptoms.dylib (1238.60.1) <5540DEA3-9C3A-3991-8C3A-7B375A5410C7> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff71ef4000 -     0x7fff71f0aff2  libsystem_trace.dylib (1147.60.3)  /usr/lib/system/libsystem_trace.dylib
    0x7fff71f0c000 -     0x7fff71f11ffb  libunwind.dylib (35.4) <769F4C16-2746-3182-85C1-45CC98D119C8> /usr/lib/system/libunwind.dylib
    0x7fff71f12000 -     0x7fff71f46ffe  libxpc.dylib (1738.61.1)  /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 92358
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=361.5M resident=0K(0%) swapped_out_or_unallocated=361.5M(100%)
Writable regions: Total=458.3M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=458.3M(100%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        1 
MALLOC                           114.1M       29 
MALLOC guard page                   24K        5 
MALLOC_MEDIUM (reserved)         336.0M        3         reserved VM address space (unallocated)
STACK GUARD                       56.0M        1 
Stack                             8192K        1 
__DATA                             693K       57 
__DATA_CONST                       156K       17 
__LINKEDIT                       353.9M       18 
__OBJC_RO                         32.0M        1 
__OBJC_RW                         1780K        2 
__TEXT                            7824K       56 
shared memory                       12K        3 
===========                     =======  ======= 
TOTAL                            910.3M      194 
TOTAL, minus reserved VM space   574.3M      194 

@nTraum as a workaround you can uninstall homebrew's perl, it will force the script to use system one (5.18.4)

[bayandin]

And there is an upstream issue https://jira.percona.com/browse/PT-1419

**Comment from Launchpad by: Carlos Salguero on: 07-04-2017 16:20:32
MacOS is not a supported platform.

https://www.percona.com/services/support/mysql-support/percona-toolkit-supported-platforms-and-versions

It seems to be a problem within your DBI::MySQL driver.
According to the attached debug, the error is here:

DBI:mysql:database;;mysql_read_default_group=client =user undef ShowErrorStatement=>1, mysql_enable_utf8=>0, PrintError=>0, AutoCommit=>1, RaiseError=>1
perl(83945,0x7fffad7943c0) malloc: * error for object 0x7f9f1ac35110: pointer being freed was not allocated

set a breakpoint in malloc_error_break to debug
Please try upgrading your DBI::MySQL driver from CPAN.

[nTraum]

Hi @bayandin,

thank you so much for the super quick response and workaround hint, I can confirm that this fixes the issue, my bad not checking the upstream issues first.

[SMillerDev]

Do you have mysql-client installed?

[nTraum]

mysql-client is installed on my machine @SMillerDev. Not sure if that was the case when I installed percona-toolkit though (in case it makes a difference).

[stale[bot]]

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

[bayandin]

Hey @nTraum, I was finally able to find a reason for the crash and fixed it in https://github.com/Homebrew/homebrew-core/pull/51180, now it's not required to uninstall homebrews perl. The PR is merged now

[nTraum]

Thank you so much @bayandin!