Yubikey not detected by gpg-agent and pcsc_scan on LMDE

I have an issue regarding the GPG agent that prevents me from using several commands and particularly the one that enforces the user to touch the key before signing. I am on Debian 8.9 / Linux Mint Debian Edition.

I have struggled to make pgp2 --edit-card work, but discovered that for reasons unknown to me I had to do it using sudo. I sent the certificates to the key and went on forcing the touch feature for them to work. The issue is that the script that enables that uses the gpg-connect-agent which never wanted to work.

Here's what I've tried so far:

$> gpg2 --card-edit
scdaemon[18891]: PC/SC OPEN failed: unknown PC/SC error code (0x8010002e)
scdaemon[18891]: PC/SC OPEN failed: unknown PC/SC error code (0x8010002e)
gpg: selecting openpgp failed: Card error
gpg: OpenPGP card not available: Card error

$> gpg --card-edit
gpg: pcsc_list_readers failed: unknown PC/SC error code (0x8010002e)
gpg: card reader not available
gpg: OpenPGP card not available: general error

$> sudo gpg --card-edit
gpg: WARNING: unsafe ownership on configuration file `/home/user/.gnupg/gpg.conf'
Application ID ...: [... bunch of data, card is properly read ...]

$> ls -lahg
-rw------- 1 user 9.0K Sep 23  2016 /home/user/.gnupg/gpg.conf // seems ok

$> gpg-connect-agent --hex "scd apdu 00 f1 00 00" /bye
gpg-connect-agent: can't connect to the agent: IPC connect call failed

$> pcsc_scan
PC/SC device scanner
V 1.4.23 (c) 2001-2011, Ludovic Rousseau <ludovic.rousseau@free.fr>
Compiled with PC/SC lite version: 1.8.11
Using reader plug'n play mechanism
Scanning present readers...
Waiting for the first reader...^C // waited ~5m, nothing came up...

$> gpg-agent --daemon
GPG_AGENT_INFO=/tmp/gpg-318mlQ/S.gpg-agent:17327:1; export GPG_AGENT_INFO;
$> GPG_AGENT_INFO=/tmp/gpg-318mlQ/S.gpg-agent:17327:1; export GPG_AGENT_INFO;

$> [ ... tried the same gpg-connect-agent && pcsc_scan, same result ]

$> gpg2 --card-edit
gpg: selecting openpgp failed: Card error
gpg: OpenPGP card not available: Card error

The card itself seems fine since using sudo and gpg --card-edit everything worked, but I have to be able to call gpg-agent as well and the issue I am facing blocks me.

If anyone could help me out on this, I'd be very grateful !

For me this was caused by ~/.gnupg/scdaemon.conf containing

disable-ccid

which is required for non-gnome wms, but apparently causes this error when using gnome. After removing it and restarting gpg-agent this issue was fixed for me