ALTER TABLE ... ROW_FORMAT=Compressed times out
Please note that I am not a MySQL developer, I use MS SQL Server.  But the behavior in your post suggests the following:

It does not look like a deadlock to me, especially with the error messages:

InnoDB: Error: semaphore wait has lasted &gt; 600 seconds
InnoDB: We intentionally crash the server, because it appears to be hung.


A deadlock normally would quickly determine which connection to roll back instead of processing up to 600 seconds before crashing the server.

Likely what is happening is that the table metadata change (the ALTER TABLE) cannot happen while there are other transactions using the table.

http://dev.mysql.com/doc/refman/5.6/en/metadata-locking.html

The link says, in part: "To ensure transaction serializability, the server must not permit one session to perform a data definition language (DDL) statement on a table that is used in an uncompleted explicitly or implicitly started transaction in another session."

EDIT: Sorry for the misunderstanding regarding deadlocks.

Per this post, https://stackoverflow.com/questions/24860111/warning-a-long-semaphore-wait

Ensure that: Innodb_adaptive_hash_index=0