ALTER TABLE times out, but does not roll back the operation

In the test case below, one connection performs ALTER, while another has something to do with statistical tables. Every ones in a while, ALTER fails with a timeout. Apparently the timeout concerns statistical tables, as there seems to be no other relation between connections. Even though the ALTER fails, the modification it performed remains, e.g. in this case the column remains renamed.

The practical effect is, for example, further replication discrepancy: since ALTER fails, it is not written in the binlog, so table remains unchanged on the slave, which causes further discrepancies.

Notes:

• the test case is very non-deterministic, run with big enough --repeat=N. Do not put it into the regression suite, create a deterministic one instead! It usually fails for me within ~20 attempts, but it can vary a lot on different machines and builds;
• sequences and prepared statement are not important, they are just used to create tables with many columns;
• tables can be (at least) MyISAM, Aria, or InnoDB, although it seems to take a bit longer with MyISAM;
• could not reproduce on the baseline.

--source include/have_sequence.inc

select concat('create table t1 (',group_concat(concat('c',seq,' int')),')') into @create_tbl from seq_1_to_300;

execute immediate @create_tbl;

create table t2 like t1;

--connect (con1,localhost,root,,)

--send

  analyze table t1 persistent for all;

--connection default

--error 0,ER_LOCK_WAIT_TIMEOUT

  alter table t2 nowait rename column c298 TO c298_renamed;

if ($mysql_errno)

{

  show create table t2;

  --die ALTER failed with ER_LOCK_WAIT_TIMEOUT, check whether `c298` column is still there

}

drop table t1, t2;

show create table t2;

Table	Create Table

t2	CREATE TABLE `t2` (

  `c1` int(11) DEFAULT NULL,

  `c2` int(11) DEFAULT NULL,

...

  `c298_renamed` int(11) DEFAULT NULL,

  `c299` int(11) DEFAULT NULL,

  `c300` int(11) DEFAULT NULL

) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci

mysqltest: At line 17: ALTER failed with ER_LOCK_WAIT_TIMEOUT, check whether `c298` column is still there