We recommend that you create an empty file called .upgrading in the $DIR_NEW directory to avoid that saphostexec starts the upgrade procedure during the extraction of SAPHOSTAGENT<SP-version>.SAR - with the consequence that only part of the newest version of the packages is upgraded.
cd /usr/sap/hostctrl/new/
touch .upgrading
SAPCAR -xvf SAPHOSTAGENT <SP-version>.SAR
rm .upgrading