This is your "Debugging Emacs 101", lesson 1:

A breakpoint in Fsignal is frequently hit because some error is thrown
which Emacs will catch and ignore, but the debugger gets to see it
first. To see whether this is the signal you are after (if you don't
already know), do this:

(gdb) p error_symbol
(gdb) xsymbol

The last command should display the Lisp name of the signal. Crystal
ball here says you will see "void-variable", which is not the signal
you want. So now make the breakpoint conditional:

(gdb) condition 3 error_symbol != 41328
(gdb) c

and see what other signal is thrown. I had a couple of other
unrelated signals (which happened once each, so I didn't feel like
making the condition more complex), and finally you will get your
expected "end-of-file" error. Then look around; the Lisp backtrace
should be the first thing to look at.

Thanks for that quick intro to setting conditional breakpoints.

I did

(gdb) condition 3 error_symbol!=<num1> && error_symbol!=<num2> && ..

and looks like that worked.

But it looks like I have a different backtrace than the one you got.

(gdb) p error_symbol

$3 = 49824

(gdb) xsymbol

$4 = (struct Lisp_Symbol *) 0xc87bd0 <lispsym+49824>

"void-variable"

(gdb) condition 3 error_symbol!=41328 && error_symbol!=49824

(gdb) c

Continuing.

Breakpoint 3, Fsignal (error_symbol=19056, data=16197139) at eval.c:1471

1471 = (NILP (error_symbol) ? Fcar (data) : error_symbol);

(gdb) p error_symbol

$5 = 19056

(gdb) xsymbol

$6 = (struct Lisp_Symbol *) 0xc803a0 <lispsym+19056>

"error"

(gdb) bt

#0 Fsignal (error_symbol=19056, data=16197139) at eval.c:1471

#1 0x00000000005f631a in Ffuncall (nargs=3, args=0x7fffffff6430) at eval.c:2696

#2 0x000000000063c073 in exec_byte_code (bytestr=9618644, vector=9618677, maxdepth=26, args_template=514, nargs=2, args=0x7fffffff6970) at bytecode.c:880

#3 0x00000000005f6b6c in funcall_lambda (fun=9618597, nargs=2, arg_vector=0x7fffffff6970) at eval.c:2855

#4 0x00000000005f6568 in Ffuncall (nargs=3, args=0x7fffffff6968) at eval.c:2742

#5 0x000000000063c073 in exec_byte_code (bytestr=26216724, vector=26182181, maxdepth=18, args_template=0, nargs=0, args=0x0) at bytecode.c:880

#6 0x00000000005f6ea8 in funcall_lambda (fun=26182285, nargs=2, arg_vector=0x18f8225) at eval.c:2921

#7 0x00000000005f6568 in Ffuncall (nargs=3, args=0x7fffffff6e98) at eval.c:2742

#8 0x000000000063c073 in exec_byte_code (bytestr=26203300, vector=26180981, maxdepth=22, args_template=0, nargs=0, args=0x0) at bytecode.c:880

#9 0x00000000005f6ea8 in funcall_lambda (fun=26181189, nargs=1, arg_vector=0x18f7d75) at eval.c:2921

#10 0x00000000005f6568 in Ffuncall (nargs=2, args=0x7fffffff73d8) at eval.c:2742

#11 0x000000000063c073 in exec_byte_code (bytestr=25712436, vector=20655013, maxdepth=26, args_template=1026, nargs=1, args=0x7fffffff7918) at bytecode.c:880

#12 0x00000000005f6b6c in funcall_lambda (fun=24354509, nargs=1, arg_vector=0x7fffffff7910) at eval.c:2855

#13 0x00000000005f6568 in Ffuncall (nargs=2, args=0x7fffffff7908) at eval.c:2742

#14 0x000000000063c073 in exec_byte_code (bytestr=17397476, vector=21453909, maxdepth=10, args_template=2, nargs=0, args=0x7fffffff7e40) at bytecode.c:880

#15 0x00000000005f6b6c in funcall_lambda (fun=20671589, nargs=0, arg_vector=0x7fffffff7e40) at eval.c:2855

#16 0x00000000005f6568 in Ffuncall (nargs=1, args=0x7fffffff7e38) at eval.c:2742

#17 0x000000000063c073 in exec_byte_code (bytestr=14902196, vector=21523493, maxdepth=22, args_template=1026, nargs=1, args=0x7fffffff8448) at bytecode.c:880

#18 0x00000000005f6b6c in funcall_lambda (fun=21523645, nargs=1, arg_vector=0x7fffffff8440) at eval.c:2855

#19 0x00000000005f6568 in Ffuncall (nargs=2, args=0x7fffffff8438) at eval.c:2742

#20 0x00000000005ee638 in Ffuncall_interactively (nargs=2, args=0x7fffffff8438) at callint.c:252

#21 0x00000000005f61e8 in Ffuncall (nargs=3, args=0x7fffffff8430) at eval.c:2673

#22 0x00000000005f09be in Fcall_interactively (function=5444288, record_flag=5289200, keys=13400757) at callint.c:840

#23 0x00000000005f6355 in Ffuncall (nargs=4, args=0x7fffffff8758) at eval.c:2700

#24 0x000000000063c073 in exec_byte_code (bytestr=10409484, vector=10409517, maxdepth=54, args_template=4102, nargs=2, args=0x7fffffff8cd8) at bytecode.c:880

#25 0x00000000005f6b6c in funcall_lambda (fun=10409437, nargs=2, arg_vector=0x7fffffff8cc8) at eval.c:2855

#26 0x00000000005f6568 in Ffuncall (nargs=3, args=0x7fffffff8cc0) at eval.c:2742

#27 0x000000000063c073 in exec_byte_code (bytestr=10408684, vector=10408717, maxdepth=62, args_template=3078, nargs=3, args=0x7fffffff9318) at bytecode.c:880

#28 0x00000000005f6b6c in funcall_lambda (fun=10408629, nargs=3, arg_vector=0x7fffffff9300) at eval.c:2855

#29 0x00000000005f6568 in Ffuncall (nargs=4, args=0x7fffffff92f8) at eval.c:2742

#30 0x00000000005ee638 in Ffuncall_interactively (nargs=4, args=0x7fffffff92f8) at callint.c:252

#31 0x00000000005f61e8 in Ffuncall (nargs=5, args=0x7fffffff92f0) at eval.c:2673

#32 0x00000000005f576f in Fapply (nargs=3, args=0x7fffffff93e0) at eval.c:2321

#33 0x00000000005eeab0 in Fcall_interactively (function=560928, record_flag=0, keys=13400757) at callint.c:389

#34 0x00000000005f6355 in Ffuncall (nargs=4, args=0x7fffffff9668) at eval.c:2700

#35 0x000000000063c073 in exec_byte_code (bytestr=10409484, vector=10409517, maxdepth=54, args_template=4102, nargs=1, args=0x7fffffff9bc0) at bytecode.c:880

#36 0x00000000005f6b6c in funcall_lambda (fun=10409437, nargs=1, arg_vector=0x7fffffff9bb8) at eval.c:2855

#37 0x00000000005f6568 in Ffuncall (nargs=2, args=0x7fffffff9bb0) at eval.c:2742

#38 0x00000000005f5d10 in call1 (fn=14784, arg1=560928) at eval.c:2552

#39 0x000000000055ac58 in command_loop_1 () at keyboard.c:1471

#40 0x00000000005f2f86 in internal_condition_case (bfun=0x55a49f <command_loop_1>, handlers=19056, hfun=0x559c89 <cmd_error>) at eval.c:1309

#41 0x000000000055a1a7 in command_loop_2 (ignore=0) at keyboard.c:1099

#42 0x00000000005f28a6 in internal_catch (tag=46224, func=0x55a17e <command_loop_2>, arg=0) at eval.c:1074

#43 0x000000000055a147 in command_loop () at keyboard.c:1078

#44 0x0000000000559858 in recursive_edit_1 () at keyboard.c:684

#45 0x00000000005599eb in Frecursive_edit () at keyboard.c:755

#46 0x00000000005578aa in main (argc=2, argv=0x7fffffffa068) at emacs.c:1606

Lisp Backtrace:

"signal" (0xffff6438)

"error" (0xffff6970)

"epg-check-configuration" (0xffff6ea0)

"epg-find-configuration" (0xffff73e0)

"package-refresh-contents" (0xffff7910)

"package-menu-refresh" (0xffff7e40)

"list-packages" (0xffff8440)

"funcall-interactively" (0xffff8438)

"call-interactively" (0xffff8760)

"command-execute" (0xffff8cc8)

"execute-extended-command" (0xffff9300)

"funcall-interactively" (0xffff92f8)

"call-interactively" (0xffff9670)

"command-execute" (0xffff9bb8)

(gdb)