Sequel Pro 1.1: Exception when mysql_upgrade has not been run after upgrading MySQL to 5.7 (homebrew) #2302

phoenixgao opened this Issue Oct 22, 2015 · 47 comments


None yet

Test connection works fine, but once connect this error happens.

(Sequel Pro installed on Mac 10.10, mysql installed on remote ubuntu 14.04 server)


*** -[NSPlaceholderString initWithString:]: nil argument

    0   CoreFoundation                      0x00007fff8e42503c __exceptionPreprocess + 172
    1   libobjc.A.dylib                     0x00007fff99e4076e objc_exception_throw + 43
    2   CoreFoundation                      0x00007fff8e424eed +[NSException raise:format:] + 205
    3   Foundation                          0x00007fff908182dc -[NSPlaceholderString initWithString:] + 102
    4   Sequel Pro                          0x000000010002e6a9 -[SPDatabaseDocument setConnection:] + 384
    5   Foundation                          0x00007fff9086bd00 __NSThreadPerformPerform + 293
    6   CoreFoundation                      0x00007fff8e341a01 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
    7   CoreFoundation                      0x00007fff8e333b8d __CFRunLoopDoSources0 + 269
    8   CoreFoundation                      0x00007fff8e3331bf __CFRunLoopRun + 927
    9   CoreFoundation                      0x00007fff8e332bd8 CFRunLoopRunSpecific + 296
    10  HIToolbox                           0x00007fff91e8356f RunCurrentEventLoopInMode + 235
    11  HIToolbox                           0x00007fff91e832ea ReceiveNextEventCommon + 431
    12  HIToolbox                           0x00007fff91e8312b _BlockUntilNextEventMatchingListInModeWithFilter + 71
    13  AppKit                              0x00007fff927469bb _DPSNextEvent + 978
    14  AppKit                              0x00007fff92745f68 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 346
    15  AppKit                              0x00007fff9273bbf3 -[NSApplication run] + 594
    16  AppKit                              0x00007fff926b8354 NSApplicationMain + 1832
    17  Sequel Pro                          0x0000000100001994 start + 52
    18  ???                                 0x0000000000000002 0x0 + 2
dmoagx commented Oct 22, 2015

Where did you install MySQL from?


Am I the only one getting this error?

I installed (upgraded) mysql by following this document:

mysql --version
mysql  Ver 14.14 Distrib 5.7.8-rc, for Linux (x86_64) using  EditLine wrapper

connect to mysql from console works fine.
When I try to connect from sequel pro, an error window pops up and sequel pro keeps the status "connecting..."
and It's empty in select datebases dropdown. But I can create a new database at that time and then all databases appears in the select dropdown.
If I click one of them I can see table list. If I click one of the tables, then sequel pro hangs.

dmoagx commented Oct 23, 2015

Using that works fine for me with 1.1

Welcome to Ubuntu 14.04.3 LTS (GNU/Linux 3.13.0-66-generic x86_64)

 * Documentation:
Last login: Fri Oct 23 16:28:06 2015
max@ubuntu:~$ mysql --version
mysql  Ver 14.14 Distrib 5.7.8-rc, for Linux (x86_64) using  EditLine wrapper

Connecting works, I can see databases and select tables, etc.

Is this a fresh install or did you upgrade from a previous version?

Dretch commented Oct 27, 2015

I am getting the same issue. I am running OS X 10.10.5 (Yosemite) with MySQL 5.7.9 (client and server both on the same OS X machine).

I upgraded MySQL from 5.6.24 by copying the data folder from the old version to the new.

dmoagx commented Oct 27, 2015

Um...that's nice and all, but if you don't provide any info for me to work with I can't help you either.

dmoagx commented Oct 27, 2015

Btw, related crash report is:

@dmoagx dmoagx added the Bug label Oct 27, 2015

@dmoagx I upgraded from a previous version, which is default version installed via apt-get install mysql-server mysql-client. (I guess it was 5.5.x?) The phpmyadmin works, even my application works btw.

I will also try to install a fresh new one to see if it solves my problem, but I think there might be other people who did upgrade would see this error too.

dmoagx commented Oct 28, 2015

Did you run the mysql_upgrade program?


Yes, I did. there was some timestamp columns default value was '0000-00-00 00:00:00' and I have to change them to default current_timestamp to complete the upgrade.

Dretch commented Oct 29, 2015


Originally I had not run mysql_upgrade. Now I have, and (after restarting MySQL), SequelPro works!

I think the problem was that the SHOW VARIABLES MySQL command was returning an error because I had not run mysql_upgrade - it was returning this error string rather than a set of variables, and Sequel Pro was choking on it:

ERROR 1682 (HY000): Native table 'performance_schema'.'session_variables' has the wrong structure

dmoagx commented Oct 29, 2015

@Dretch Thanks, that's something I can look into.

@dmoagx dmoagx removed the WaitingOnUser label Oct 29, 2015
dmoagx commented Oct 29, 2015

OK, I could reproduce the issue by just replacing a mysql 5.5 server with 5.7 without properly upgrading.

I actually thought we had already fixed that issue (for another reason) but it looks like c7b5e88 did not make it into the 1.1 branch.

dmoagx commented Oct 30, 2015

Fixed in d82dc7b for the 1.1.x branch

@dmoagx dmoagx added this to the 1.1.1 milestone Oct 30, 2015
Dretch commented Oct 30, 2015

Thanks !
El 30/10/2015 1:00 a. m., "Max Lohrmann"

Fixed in d82dc7b
for the 1.1.x branch

Reply to this email directly or view it on GitHub
#2302 (comment)

vihuvac commented Nov 18, 2015

I got the same error, Sequel Pro just stopped working even when it was working fine:

MySQL (installed via homebrew): mysql Ver 14.14 Distrib 5.7.9, for osx10.11 (x86_64) using EditLine wrapper

OS: Mac OS X 10.11.1 El Capitan


Same error too, i'm using mysql installed via homebrew and OSX El Capitan


OS X El Capitan + homebrew + MySQL 5.7.9:
The fix was to run:
mysql_upgrade -u root -p
mysql.server restart

vihuvac commented Nov 20, 2015

@giannisp awesome, it worked! Thank you very much 👍


�The error is because an old version server was not properly upgraded to 5.7.

To fix it need to run
manually fix some fields if needed
and then restart mysql server

@phoenixgao phoenixgao closed this Nov 20, 2015

worked like a charm, awesome!


knilob commented Nov 20, 2015

Thanks, @giannisp. Running the mysql_upgrade command totally did the trick.

Alhadis commented Nov 25, 2015

@giannisp: You ripper! :D That fix worked a treat, thanks cobber! 👍

I also have MySQL managed by Homebrew, so perhaps a recent update had something to do with it...?


Yes, it's worked. Thanks @giannisp . 🚀


I had the same issue, none of the methods above worked, completely reinstalling the MySQL from homebrew fixed the issue for my case:

brew uninstall mysql
rm -Rf /usr/local/var/mysql
brew install mysql
mysql.server start
@dmoagx dmoagx reopened this Dec 3, 2015

I am on El Capitan and MySQL installed via homebrew. @giannisp's solution did it for me! Thanks.

LucasKA commented Dec 9, 2015

+1 to @giannisp

Same issue

bramchi commented Dec 9, 2015

@giannisp great tip, worked for me too

karolyi commented Dec 13, 2015

+1, mysql_upgrade + restart fixed it, thx for the clarification

@dmoagx dmoagx changed the title from Sequel Pro 1.1 encountered an unexpected error when connecting to mysql 5.7.8 rc via ssh to Sequel Pro 1.1: Exception when mysql_upgrade has not been run after upgrading MySQL to 5.7 (homebrew) Dec 13, 2015
vaske commented Jan 4, 2016

@giannisp thanks man!

azharp commented Jan 7, 2016

many thanks! just saved my day.

Elyx0 commented Jan 11, 2016

Saved my day too ! Pasted my exception *** -[NSPlaceholderString initWithString:]: nil argument sequelpro and ended up here. Thanks again.


@giannisp Thank you, these commands fixed the issue!

mysql_upgrade -u root -p
mysql.server restart
ciarant commented Jan 13, 2016

@giannisp Thank you!

taledo commented Jan 17, 2016

Glad I found this! The mysql_upgrade did the trick 👍


Same here, i have a homebrew installed mysql (5.7.10) and after a mysql_upgrade and mysql.server restart everything is working again ;-)

Jatiba commented Feb 2, 2016

@giannisp Thank you, mysql_upgrade did the trick!
MacOS X 10.11.3 - Sequel Pro crashes after homebrew update of MySQL.


Thanks you @giannisp !

resting commented Feb 8, 2016

Thanks. mysql_upgrade -uroot did the trick for me.
Had to restart mysql after upgrade and boom!


Guys, I'm still getting the same error when I try to connect with a user that is not root, if I connect with the root user everything works perfectly but the moment I try to connect with a user that has only access to one database even tho connecting with that user from the console works perfectly using sequel Pro I get the same error reported here. Tried the mysql_upgrade -uroot -p and restarted but still having the same issue.

Sequel Pro
MySQL 5.7.8-rc
Ubuntu 14.04.3


Just downloaded the RC1a version from here: and now it works perfectly.

dmoagx commented Feb 13, 2016

@jsoprano Nevertheless, please open and look for messages from Sequel Pro, there is still a high chance something is not right.


@dmoagx just tested closing Sequel Pro, tailing the /var/log/system.log file and opening the app and connecting again and didn't find any logs written, should I be looking in a different log or that its ok?

dmoagx commented Feb 13, 2016

system.log is fine usually.
If nothing is logged then your issue probably had a different cause - which would also match with mysql_upgrade not fixing the problem for you.
Do you still have a full crash report?


@dmoagx yes, I did report it today the last time that it happened but I also have the crash report file or contents if you want me to mail it or paste it here, just let me know what you prefer.


I received the same error after upgrading from 5.5 --> 5.6 --> 5.7.11 on Ubuntu 14.04. This worked for me:

root@server $ mysql_upgrade -uroot -p
root@server $ sudo service mysql restart

dmoagx commented Feb 20, 2016
@dmoagx dmoagx closed this Feb 20, 2016
realwol commented Sep 28, 2016

Thanks a lot.

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