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EXCEPTION_ACCESS_VIOLATION #59

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anthonyagudelox3 opened this issue Jun 19, 2019 · 7 comments
Closed

EXCEPTION_ACCESS_VIOLATION #59

anthonyagudelox3 opened this issue Jun 19, 2019 · 7 comments

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@anthonyagudelox3
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anthonyagudelox3 commented Jun 19, 2019 •
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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
@DilumAluthge
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May be an issue with the garbage collector.

Before you run any code, run this command: Base.GC.enable(false)

Then run your code.

And then after you have run your code, run this command: Base.GC.enable(true)

@anthonyagudelox3
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May be an issue with the garbage collector.

Before you run any code, run this command: Base.GC.enable(false)

Then run your code.

And then after you have run your code, run this command: Base.GC.enable(true)

Okay I tried it and it still is giving me the same issue.

@DilumAluthge
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Hmmm. Okay so we need to figure out whether this is a problem with BioMedQuery.jl or MySQL.jl.

Instead of using BioMedQuery, use MySQL.jl directly and see if it works. This example code might help: https://github.com/JuliaDatabases/MySQL.jl#example

@anthonyagudelox3
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Running the following gives a similar error:
MySQL.Query(con, command) |> DataFrame

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}}(MySQL.Result(Ptr{Nothing} @0x00eac8e0), Ptr{Ptr{Int8}} @0x250e7f60, 3, 2294)

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-f9149ad6a13ab84805b2ee55adc59766:23
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: 10EC1012)
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
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: 1F4C288F)
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: 10E3BD31)
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_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]
macro expansion at C:\Users\Thor.julia\packages\Media\ItEPc\src\dynamic.jl:24 [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_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: 10E7182A)
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: 10E6FBD6)
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: 67020851 (Pool: 67017371; Big: 3480); GC: 360

However running
MySQL.Query(con, command)
gives this result: MySQL.Query{true,(:pmid, :hgnc_id, :count),Tuple{Union{Missing, Int32},Union{Missing, Int32},Int64}}(MySQL.Result(Ptr{Nothing} @0x1148eec8), Ptr{Ptr{Int8}} @0x199dc1e8, 3,
2294)

@DilumAluthge
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Hmmm, so just to summarize.

This works: MySQL.Query(con, command)

This does not work: MySQL.Query(con, command) |> DataFrame

Is that correct?

@DilumAluthge
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If that’s the case, then this is either an issue with the MySQL.jl package or the DataFrames.jl package. I’d recommend that you open issues on both of those repositories.

@DilumAluthge
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Doesn’t seem like an issue with BioMedQuery.jl though, so I’ll close this issue.

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@DilumAluthge @anthonyagudelox3