Using Heimdall v1.4 RC1 to flash Clockworkmod Recovery on a Samsung S4, I get the following,
$ sudo heimdall flash --RECOVERY ./recovery.img --no-reboot
Heimdall v1.4 RC1
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Initialising connection...
Detecting device...
Claiming interface...
Attempt failed. Detaching driver...
Claiming interface again...
Setting up interface...
Checking if protocol is initialised...
Protocol is not initialised.
Initialising protocol...
Protocol initialisation successful.
Beginning session...
Session begun.
In certain situations this device may take up to 2 minutes to respond.
Please be patient!
Downloading device's PIT file...
PIT file download successful.
Uploading RECOVERY
100%
ERROR: Failed to confirm end of file transfer sequence!
ERROR: RECOVERY upload failed!
Ending session...
Releasing device interface...
Re-attaching kernel driver...
I've even tried two different builds of Clockworkmod,
-rw-rw-r-- 1 ecarroll ecarroll 6.8M Aug 11 23:23 clockworkmod_6.0.3.2_jfltespr.img
-rw-rw-r-- 1 ecarroll ecarroll 6.8M Aug 12 00:02 recovery-clockwork-6.0.3.2-jfltespr.img
$ md5sum *clock*
c95fac4d0e27fcb0c3355f209e62cd9c clockworkmod_6.0.3.2_jfltespr.img
760cbf5a3b157ab23f49fcf40b46db2f recovery-clockwork-6.0.3.2-jfltespr.img
Answer
This is a because of a bug in Heimdall v1.4 RC1 -- the version that shipped with Ubuntu 13.04. What you'll want to do is upgrade Heimdall to version 1.4 final, or the latest version..
That should do it. Run heimdall info | head -n1 to get your current version.
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