diff --git a/R/templates/update_r_packages.sh.j2 b/R/templates/update_r_packages.sh.j2
index c498d037..83aaa977 100644
--- a/R/templates/update_r_packages.sh.j2
+++ b/R/templates/update_r_packages.sh.j2
@@ -139,7 +139,11 @@ function debian_pkgs() {
         else
             logger "update_r_packages: APT cache not updated"
         fi
-        xargs -a <(awk '/^\s*[^#]/' "$PKGS_LIST") -r -- apt-get install -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >/var/log/update_r_debs.log 2>&1
+        >/var/log/update_r_debs.log
+        while read deb_pkg ; do
+            apt-get install ${deb_pkg} -q -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >>/var/log/update_r_debs.log 2>&1
+        done < $PKGS_LIST
+        apt-get autoremove -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" >> /var/log/update_r_debs.log 2>&1
     else
         logger "update_r_packages: skipping the debian packages installation"
     fi