As written in the announcement of the GnuPG >=2.1.13 release:
If a /run/user/$UID directory exists, that directory is now used for IPC sockets instead of the GNUPGHOME directory. This fixes problems with NFS and too long socket names and thus avoids the need for redirection files.
A workaround is to put export GNUPGHOME=/run/user/id -u/gnupg in your ~/.profile.