El Capitan can´t see or remove partition but it shows up in Terminal
It is because the Linux file system is something that OS X cannot natively read.  The easiest thing to do is to is load up a live Linux CD and change the partition to something OS X can read like ExFAT, or MSDOS.  Once that change has been made, OS X should be able to see it; allowing you to manipulate the partition.

The other option is to load up FUSE for OS X which will allow you to read/write ext2, ext3, and ext4 file systems.  I am not a fan of loading up applications for one time use, but I wanted to let you know about it.