EXCEPTION_ACCESS_VIOLATION

[anthonyagudelox3]

Hello, I am trying to use MySQL to access my local database and submit a query, however when I run the following code I get this error. This seems like a privileges issue however, I am unsure on how to resolve it.
This was done on Julia v0.7.0, on a Windows 10 PC.

`
analysis = "ptb"
con = MySQL.connect("127.0.0.1", "root", password, db = "$(analysis)_pubmed")

command = """SELECT DISTINCT g.pmid, g.hgnc_id, count(*) as count
FROM pubtator_genes g
WHERE g.passage_type="abstract"
GROUP BY g.pmid, g.hgnc_id
ORDER BY count;"""

abstract_df = BioMedQuery.DBUtils.db_query(con, command)
`

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x6fc4ce0b -- jl_get_nth_field at /home/Administrator/buildbot/worker/package_win32/build/src\datatype.c:837
in expression starting at untitled-f9149ad6a13ab84805b2ee55adc59766:19
jl_get_nth_field at /home/Administrator/buildbot/worker/package_win32/build/src\datatype.c:837
jl_f_getfield at /home/Administrator/buildbot/worker/package_win32/build/src\builtins.c:757
getproperty at C:\Users\Thor.julia\packages\Tables\0M7Kt\src\utils.jl:27 [inlined]
macro expansion at C:\Users\Thor.julia\packages\Tables\0M7Kt\src\utils.jl:55 [inlined]
eachcolumn at C:\Users\Thor.julia\packages\Tables\0M7Kt\src\utils.jl:47
unknown function (ip: 10DDF932)
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
buildcolumns at C:\Users\Thor.julia\packages\Tables\0M7Kt\src\fallbacks.jl:95 [inlined]
columns at C:\Users\Thor.julia\packages\Tables\0M7Kt\src\fallbacks.jl:149 [inlined]
Type at C:\Users\Thor.julia\packages\DataFrames\IKMvt\src\other\tables.jl:21
jl_fptr_args at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1839
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
|> at .\operators.jl:813
jl_fptr_args at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1839
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
db_query at C:\Users\Thor.julia\packages\BioMedQuery\K4kwC\src\DBUtils\mysql_db_utils.jl:87
jl_fptr_args at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1839
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
do_call at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:324
eval_value at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:428
eval_stmt_value at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:363 [inlined]
eval_body at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:682
jl_interpret_toplevel_thunk_callback at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:799
unknown function (ip: FFFFFFFE)
unknown function (ip: 1726EA9F)
unknown function (ip: 00000001)
jl_interpret_toplevel_thunk at /home/Administrator/buildbot/worker/package_win32/build/src\interpreter.c:808
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win32/build/src\toplevel.c:831
jl_parse_eval_all at /home/Administrator/buildbot/worker/package_win32/build/src\ast.c:841
jl_load_file_string at /home/Administrator/buildbot/worker/package_win32/build/src\ast.c:871
include_string at .\loading.jl:1002
include_string at C:\Users\Thor.julia\packages\CodeTools\xGemk\src\eval.jl:30
unknown function (ip: 10DA2EF1)
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
#116 at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:94
withpath at C:\Users\Thor.julia\packages\CodeTools\xGemk\src\utils.jl:30
withpath at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:46 [inlined]
#115 at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:93 [inlined]
with_logstate at .\logging.jl:397
with_logger at .\logging.jl:493 [inlined]
#114 at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:92 [inlined]
hideprompt at C:\Users\Thor.julia\packages\Atom\OZKl0\src\repl.jl:87
jl_fptr_args at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1839
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
macro expansion at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:91 [inlined]
#113 at C:\Users\Thor.julia\packages\Atom\OZKl0\src\eval.jl:86
jl_fptr_args at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1839
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:1829
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
handlemsg at C:\Users\Thor.julia\packages\Atom\OZKl0\src\comm.jl:164
unknown function (ip: 10D85D2A)
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
jl_apply at /home/Administrator/buildbot/worker/package_win32/build/src\julia.h:1538 [inlined]
jl_f__apply at /home/Administrator/buildbot/worker/package_win32/build/src\builtins.c:563
#19 at .\task.jl:262
unknown function (ip: 10D82BB6)
jl_apply_generic at /home/Administrator/buildbot/worker/package_win32/build/src\gf.c:2182
jl_apply at /home/Administrator/buildbot/worker/package_win32/build/src\julia.h:1538 [inlined]
start_task at /home/Administrator/buildbot/worker/package_win32/build/src\task.c:268
wmain at /home/Administrator/buildbot/worker/package_win32/build/ui\repl.c:233
Allocations: 37273076 (Pool: 37270984; Big: 2092); GC: 195

[anthonyagudelox3]

Is anybody watching this?

[quinnj]

Yes, I'll see if I can dig into this today.

[quinnj]

@anthonyagudelox3, could you run the following and share the output?

q = MySQL.Query(con, command)
dump(q)

[anthonyagudelox3]

I ran the code;

q = MySQL.Query(con, command)
dump(q)

And this is the result;

WARNING: both DataFrames and Base export "showall"; uses of it in module Main must be qualified
MySQL.Query{true,(:pmid, :hgnc_id, :count),Tuple{Union{Missing, Int32},Union{Missing, Int32},Int64}}
  result: MySQL.Result
    ptr: Ptr{Nothing} @0x0ea62400
  ptr: Ptr{Ptr{Int8}} @0x2245b120
  ncols: Int32 3
  nrows: Int32 2294

[quinnj]

Hmmm, I can't seem to reproduce this at all. Have you tried the query on a newer release of Julia? 1.0, 1.1, or the soon to be released 1.2? (all available here). In general, Julia 0.7 is not well-supported since it was only a transition release to port code from 0.6 to 1.0; hence, 1.0 (1.0.4 technically) has a number of bugfixes that are not included in 0.7. The reason I mention all this is that it seems like this is a core language problem as opposed to a MySQL.jl problem.

Now, if you can reproduce on a newer version of Julia, the 2nd thing to try is to master of this package, since there have also been fixes merged since the latest release; to try master, you can do ] add MySQL#master from the Julia repl.

Let me know if you can still reproduce the issue after those upgrades and we can figure out how to further debug this and figure out what's causing the issue.

[anthonyagudelox3]

Hey @quinnj it looks like I can't reproduce the issue on Julia 1.1.1. Thank you for your time, I will start updating the code to work on Julia 1.1.1.

[quinnj]

That's great to hear; did you by chance happen to try the code on Julia 1.0.4? (the current LTS release). My guess is it works there too, but just wondered if you tried.

[anthonyagudelox3]

I have not tried it on Julia 1.0.4 yet unfortunately.