In particular, it is the charon profile which doesn't allow access to the PC/SC layer and to the specific smartcard files (depending on the vendor).
For example, with a Gemalto IDPrime .NET card, this is what I get in my logs:
#Jun 29 08:29:46 ubuntu kernel: [ 873.811807] type=1400 audit(1435559386.465:51): apparmor="DENIED" operation="open" profile="/usr/lib/ipsec/charon" name="/run/shm/gemalto_idprime_sdata" pid=11356 comm="charon" requested_mask="rwc" denied_mask="rwc" fsuid=0 ouid=0 #Jun 29 08:29:46 ubuntu kernel: [ 873.817301] type=1400 audit(1435559386.469:52): apparmor="DENIED" operation="connect" profile="/usr/lib/ipsec/charon" name="/run/pcscd/pcscd.comm" pid=11356 comm="charon" requested_mask="rw" denied_mask="rw" fsuid=0 ouid=0
In particular, it is the charon profile which doesn't allow access to the PC/SC layer and to the specific smartcard files (depending on the vendor).
For example, with a Gemalto IDPrime .NET card, this is what I get in my logs:
#Jun 29 08:29:46 ubuntu kernel: [ 873.811807] type=1400 audit(143555938 6.465:51) : apparmor="DENIED" operation="open" profile= "/usr/lib/ ipsec/charon" name="/ run/shm/ gemalto_ idprime_ sdata" pid=11356 comm="charon" requested_ mask="rwc" denied_mask="rwc" fsuid=0 ouid=0 6.469:52) : apparmor="DENIED" operation="connect" profile= "/usr/lib/ ipsec/charon" name="/ run/pcscd/ pcscd.comm" pid=11356 comm="charon" requested_mask="rw" denied_mask="rw" fsuid=0 ouid=0
#Jun 29 08:29:46 ubuntu kernel: [ 873.817301] type=1400 audit(143555938