We have also run into a possible mysql bug related to indexing starting in version 5.6.29. The symptom is similar to your report and we saw this sort of error in the mysql log:

InnoDB: Assertion failure in thread 140011690678016 in file row0merge.cc line 794


At the time our solution was to revert back to mysql 5.6.28 which didn't have the issue. We don't know yet if this is fixed in a newer release.

On 10/14/16 1:29 AM, Alex Vandiver wrote:
On Thu, 13 Oct 2016 20:32:36 +0000
James Zuelow <james.zue...@juneau.org> wrote:
Package versions at the moment are MySQL 5.6.30, Perl 5.2.22, and
request-tracker 4.2.13.  There is a Perl 5.4 upgrade available, but
that breaks my rt4 installation.

For reference, your perl versions are not comprehensible.  Wheezy ships
perl 5.14.2, per https://packages.debian.org/wheezy/perl, and there has
never been a perl version 5.2 or 5.4 -- 5.002 was released in 1996,
5.004 in 1997, and 5.6 in 2000.


Indexing existing data...
Going to run the following in the DB:
     CREATE FULLTEXT INDEX AttachmentsIndex ON AttachmentsIndex(Content)

[58876] [Thu Oct 13 02:23:42 2016] [warning]: DBD::mysql::db do failed:
Lost connection to MySQL server during query at
./rt-setup-fulltext-index line 736, <STDIN> line 2.

Check your "max_allowed_packet" setting in mysqld.  The most common
cause is the MySQL client (here, rt-fulltext-indexer) sending something
in the MySQL wire protocol which is larger than that limit, which
causes the server to unceremoniously drop the connection.

Raise that limit and restart mysql, and it should resolve the issue.

 - Alex
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---------
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https://bestpractical.com/training
* Boston - October 24-26
* Los Angeles - Q1 2017

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