Tested on GnuPG 2.1.9. Fixes hang when using gpg-agent with YubiKeys on OS X. Port of https://github.com/GPGTools/MacGPG2/blob/6b5a3c/Formula/Patches/gnupg2/pcsc-wrapper.patch

gnupg21-pcsc-wrapper-hang.patch

--- a/scd/apdu.c	2015-10-17 22:25:39.000000000 +0100
+++ b/scd/apdu.c	2015-10-17 22:29:52.000000000 +0100
@@ -29,6 +29,7 @@
 #include <string.h>
 #include <assert.h>
 #include <signal.h>
+#include <pthread.h>
 #ifdef USE_NPTH
 # include <unistd.h>
 # include <fcntl.h>
@@ -944,6 +945,23 @@


 #ifndef NEED_PCSC_WRAPPER
+struct myArgs {
+    long pcsc_context;
+    struct pcsc_readerstate_s *rdrstates;
+    pthread_cond_t cond;
+    long err;
+};
+
+// Helper Thread to have a timeout for pcsc_get_status_change.
+void *get_status_change_thread (void *pointer) {
+    struct myArgs *args = pointer;
+    args->err = pcsc_get_status_change (args->pcsc_context,
+                                        0,
+                                        args->rdrstates, 1);
+    pthread_cond_signal(&args->cond);
+    return NULL;
+}
+
 static int
 pcsc_get_status_direct (int slot, unsigned int *status)
 {
@@ -953,9 +971,32 @@
   memset (rdrstates, 0, sizeof *rdrstates);
   rdrstates[0].reader = reader_table[slot].rdrname;
   rdrstates[0].current_state = PCSC_STATE_UNAWARE;
-  err = pcsc_get_status_change (reader_table[slot].pcsc.context,
-                                0,
-                                rdrstates, 1);
+
+  pthread_t thread;
+  struct myArgs args;
+  args.rdrstates = rdrstates;
+  args.pcsc_context = reader_table[slot].pcsc.context;
+
+  pthread_cond_init(&args.cond, NULL);
+  pthread_create(&thread, NULL, get_status_change_thread, &args);
+
+  static struct timespec time_to_wait = {0, 0};
+  time_to_wait.tv_sec = time(NULL) + 5;
+
+  pthread_mutex_t lock;
+  pthread_mutex_init(&lock, NULL);
+  pthread_mutex_lock(&lock);
+  err = pthread_cond_timedwait(&args.cond, &lock, &time_to_wait);
+  pthread_mutex_unlock(&lock);
+
+  if (err) {
+    pthread_cancel(thread);
+    err = PCSC_E_TIMEOUT;
+  } else {
+    pthread_join(thread, NULL);
+    err = args.err;
+  }
+
   if (err == PCSC_E_TIMEOUT)
     err = 0; /* Timeout is no error error here. */
   if (err)