search

akhikolla / RcppDeepState

RcppDeepState, a simple way to fuzz test code in Rcpp packages
https://akhikolla.github.io./
8 stars 2 forks source link

Unable to extract the line without a pattern #35

Closed akhikolla closed 3 years ago

akhikolla commented 4 years ago

Hello @tdhock,

I am trying to extract the error message from the log along with the line where the error occurred.

The code I wrote doesn't read all the error messages it reads the first error message only although I specified to read all the error messages. Can you please help me find where I am going wrong? I tried debugging the code but couldn't figure out where the mistake is.

   display.dt <- nc::capture_all_str(
      logfile,
      inputs="(?:[a-zA-Z ]+values:(?:.*\n)*?)inputends\n+",
      errortrace="(?:.*\n)*?",
      "==[0-9]+== HEAP SUMMARY:",
      "\n",
      heapsum="(?:.*\n)*?",
      "==[0-9]+== LEAK SUMMARY:",
      "\n",
      leaksum="(?:.*\n)*?",
      "==[0-9]+== ERROR SUMMARY:") 

    files.list<-nc::capture_all_str(logfile,"Command: ./",
                                    file.name=".*",
                                    "_DeepState_TestHarness")
    Testharness <- paste0("DeepState_Test_",basename(dirname(logfile)),
                          "_deepstate_test_",files.list$file.name,"_test")
trace <- gsub("==[0-9]+== Warning:.*?\\n","",display.dt$errortrace)

for(trace.i in seq_along(trace)){
file.line.dt <- nc::capture_all_str(
    trace[[trace.i]],
    "==[0-9]+==",
    val="(?:(?!at|by).)*\n",
    "==[0-9]+== ","\\s*",
    data=".*\n",
    ".*",
    Testharness)
}

For log data below, I get the following output

>file.line.dt
                         val
1:  Invalid read of size 8\n
2:  Invalid read of size 8\n
                                                                                                                                                                   data
1: at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n
2: at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n

Required output:

> file.line.dt
                         val
1:  Invalid read of size 8\nAddress 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd\n
2:  Invalid read of size 8\nAddress 0xb989cd8 is 0 bytes after a block of size 648 alloc'd\n
                                                                                                                                                                   data
1: at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n  by 0x42BC7E: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:18)
2: at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n    by 0x42BCC7: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:19)

Log data

==10915== Invalid read of size 8
==10915==    at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)
==10915==    by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28)
==10915==    by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7)
==10915==    by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==  Address 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd
==10915==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==10915==    by 0x4FB8633: Rf_allocVector3 (memory.c:2766)
==10915==    by 0x42C17A: void Rcpp::Vector<14, Rcpp::PreserveStorage>::import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&, Rcpp::traits::integral_constant<bool, false>) (Vector.h:1070)
==10915==    by 0x42C021: Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&) (Vector.h:165)
==10915==    by 0x42BC7E: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:18)
==10915==    by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28)
==10915==    by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7)
==10915==    by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915== 
==10915== Invalid read of size 8
==10915==    at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)
==10915==    by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28)
==10915==    by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7)
==10915==    by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==  Address 0xb989cd8 is 0 bytes after a block of size 648 alloc'd
==10915==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==10915==    by 0x4FB8633: Rf_allocVector3 (memory.c:2766)
==10915==    by 0x42C17A: void Rcpp::Vector<14, Rcpp::PreserveStorage>::import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&, Rcpp::traits::integral_constant<bool, false>) (Vector.h:1070)
==10915==    by 0x42C021: Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&) (Vector.h:165)
==10915==    by 0x42BCC7: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:19)
==10915==    by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28)
==10915==    by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7)
==10915==    by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==    by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness)
==10915==

Thanks

tdhock commented 4 years ago

hi can you please clarify what you want? I don't see the problem. Aren't there two error messages in that log, and you are getting two rows?

On Mon, Aug 24, 2020 at 4:24 PM Akhila Chowdary Kolla < notifications@github.com> wrote:

Hello @tdhock https://github.com/tdhock,

I am trying to extract the error message from the log along with the line where the error occurred.

The code I wrote doesn't read all the error messages it reads the first error message only although I specified to read all the error messages. Can you please help me find where I am going wrong? I tried debugging the code but couldn't figure out where the mistake is.

display.dt <- nc::capture_all_str( logfile, inputs="(?:[a-zA-Z ]+values:(?:.\n)?)inputends\n+", errortrace="(?:.\n)?", "==[0-9]+== HEAP SUMMARY:", "\n", heapsum="(?:.\n)?", "==[0-9]+== LEAK SUMMARY:", "\n", leaksum="(?:.\n)?", "==[0-9]+== ERROR SUMMARY:")

files.list<-nc::capture_all_str(logfile,"Command: ./",
                                file.name=".*",
                                "_DeepState_TestHarness")
Testharness <- paste0("DeepState_Test_",basename(dirname(logfile)),
                      "_deepstate_test_",files.list$file.name,"_test")

trace <- gsub("==[0-9]+== Warning:.*?\n","",display.dt$errortrace)

for(trace.i in seq_along(trace)){ file.line.dt <- nc::capture_all_str( trace[[trace.i]], "==[0-9]+==", val="(?:(?!at|by).)\n", "==[0-9]+== ","\s", data=".\n", ".", Testharness) }

For log data below, I get the following output

file.line.dt val 1: Invalid read of size 8\n 2: Invalid read of size 8\n data 1: at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n 2: at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n

Required output:

file.line.dt val 1: Invalid read of size 8\nAddress 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd\n 2: Invalid read of size 8\nAddress 0xb989cd8 is 0 bytes after a block of size 648 alloc'd\n data 1: at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n by 0x42BC7E: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:18) 2: at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)\n by 0x42BCC7: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:19)

Log data

==10915== Invalid read of size 8 ==10915== at 0x42BD5A: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22) ==10915== by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28) ==10915== by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7) ==10915== by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== Address 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd ==10915== at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10915== by 0x4FB8633: Rf_allocVector3 (memory.c:2766) ==10915== by 0x42C17A: void Rcpp::Vector<14, Rcpp::PreserveStorage>::import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&, Rcpp::traits::integral_constant<bool, false>) (Vector.h:1070) ==10915== by 0x42C021: Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&) (Vector.h:165) ==10915== by 0x42BC7E: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:18) ==10915== by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28) ==10915== by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7) ==10915== by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== ==10915== Invalid read of size 8 ==10915== at 0x42BD92: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22) ==10915== by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28) ==10915== by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7) ==10915== by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== Address 0xb989cd8 is 0 bytes after a block of size 648 alloc'd ==10915== at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10915== by 0x4FB8633: Rf_allocVector3 (memory.c:2766) ==10915== by 0x42C17A: void Rcpp::Vector<14, Rcpp::PreserveStorage>::import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&, Rcpp::traits::integral_constant<bool, false>) (Vector.h:1070) ==10915== by 0x42C021: Rcpp::Vector<14, Rcpp::PreserveStorage>::Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> >(Rcpp::VectorBase<14, true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > const&) (Vector.h:165) ==10915== by 0x42BCC7: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:19) ==10915== by 0x40A690: DeepState_Test_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:28) ==10915== by 0x40A348: DeepState_Run_AGread_deepstate_test_get_VM_C_test() (get_VM_C_DeepState_TestHarness.cpp:7) ==10915== by 0x406CD3: DeepState_RunTest.isra.6 (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4153EA: DeepState_FuzzOneTestCase (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x4154FF: DeepState_Fuzz (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915== by 0x40781D: main (in /home/akhila/Documents/compileAttributescheck/AGread/inst/testfiles/get_VM_C/get_VM_C_DeepState_TestHarness) ==10915==

Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/akhikolla/RcppDeepState/issues/35, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHDX4XUL2CKTBXESIAVBDDSCLZDJANCNFSM4QKARX2Q .

akhikolla commented 4 years ago

Hello @tdhock ,

We have two error messages in the log but I am able to extract only one error message i.e (Invalid read of size 4 and its error line) I got something like Invalid read of size 8\n and its corresponding error line I am not getting the Address 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd\n and its corresponding error line(which is also a part of the error message) for the log:

I wrote the code to read the lines that don't start with at|by (that is the error message-Invalid read of size 8\n, Address 0xb8d7ce8 is 0 bytes after a block of size 184 alloc'd\n) and for that I am trying to get the corresponding line where the error occurred.

file.line.dt <- nc::capture_all_str(
    trace[[trace.i]],
    "==[0-9]+==",
    val="(?:(?!at|by).)*\n",
    "==[0-9]+== ","\\s*",
    data=".*\n",
    ".*",
    Testharness)

Please find the attached log error.log.txt

tdhock commented 4 years ago

Hi I think it would be easier if you add "input starts" as in the modified log file 2020-08-25.log I'm using this R code:

## add \n\ninput starts?
messages.raw <- nc::capture_all_str(
  "2020-08-25.log",
  "input starts\n",
  inputs="(?:.*\n)+?",
  "input ends\n",
  rest="(?:.+\n)+")
str(messages.raw)
messages.raw[, message.i := 1:.N]
## using tibble for the compact print method.
tibble::tibble(messages.raw)

prefix <- function(after){
  list("==[0-9]+==", after)
}
trace.pattern <- nc::quantifier(
  prefix("    "),
  "(?:at|by).*\n",
  "+")
tibble::tibble(nc::capture_all_str(
  messages.raw[2, rest],
  prefix(" "),
  problem="[^ \n].*",
  "\n",
  problem.trace=trace.pattern,
  prefix("  "),
  address=".*",
  "\n",
  address.trace=trace.pattern))

values.dt <- nc::capture_all_str(
  messages.raw[2, inputs],
  variable=".*?",
  " ",
  nc::field("values", ": ", ".*"))
tibble::tibble(values.dt)
scan(text=values.dt[1, values], quiet=TRUE)

arg.list <- list()
for(arg.i in 1:nrow(values.dt)){
  arg.row <- values.dt[arg.i]
  v <- arg.row[["variable"]]
  ## Q: how are you going to read values (line of code below) for
  ## types other than NumericVector? 
  arg.list[[v]] <- scan(
    text=arg.row[["values"]], quiet=TRUE)
}

messages.parsed <- messages.raw[, {
  values.dt <- nc::capture_all_str(
    inputs,
    variable=".*?",
    " ",
    nc::field("values", ": ", ".*"))
  arg.list <- list()
  for(arg.i in 1:nrow(values.dt)){
    arg.row <- values.dt[arg.i]
    v <- arg.row[["variable"]]
    ## Q: how are you going to read values (line of code below) for
    ## types other than NumericVector? 
    arg.list[[v]] <- scan(
      text=arg.row[["values"]], quiet=TRUE)
  }
  problems.dt <- nc::capture_all_str(
    rest,
    prefix(" "),
    problem="[^ \n].*",
    "\n",
    problem.trace=trace.pattern,
    prefix("  "),
    address=".*",
    "\n",
    address.trace=trace.pattern)
  data.table::data.table(
    arguments=list(arg.list),
    problems=list(problems.dt))
}, by=.(message.i)]

str(messages.parsed)
for(message.i in 1:nrow(messages.parsed)){
  cat(sprintf("\nmessage=%d\n", message.i))
  str(messages.parsed[["arguments"]][[message.i]])
  print(tibble::tibble(messages.parsed[["problems"]][[message.i]]))
}

The output I get from the last block is:

> for(message.i in 1:nrow(messages.parsed)){
+   cat(sprintf("\nmessage=%d\n", message.i))
+   str(messages.parsed[["arguments"]][[message.i]])
+   print(tibble::tibble(messages.parsed[["problems"]][[message.i]]))
+ }

message=1
List of 3
 $ x: num [1:80] -Inf -4.30e-277 NaN -Inf 3.92e-233 ...
 $ y: num [1:89] -Inf NaN NaN -Inf NaN ...
 $ z: num [1:72] NaN -Inf -Inf NaN NaN ...
# A tibble: 1 x 4
  problem    problem.trace             address          address.trace           
  <chr>      <chr>                     <chr>            <chr>                   
1 Invalid r… "==10904==    at 0x42BD9… Address 0xba097… "==10904==    at 0x4C2F…

message=2
List of 3
 $ x: num [1:89] -Inf NaN -Inf -7.22e-197 -1.86e+218 ...
 $ y: num [1:17] NaN NaN -Inf NaN NaN ...
 $ z: num [1:75] NaN -Inf Inf -4.59e+197 Inf ...
# A tibble: 2 x 4
  problem    problem.trace             address          address.trace           
  <chr>      <chr>                     <chr>            <chr>                   
1 Invalid r… "==10915==    at 0x42BD5… Address 0xb8d7c… "==10915==    at 0x4C2F…
2 Invalid r… "==10915==    at 0x42BD9… Address 0xb989c… "==10915==    at 0x4C2F…
>

Does that help? Also note in my code I use scan to turn the values from a character string into a numeric vector... these are numeric vectors right? See also #38

tdhock commented 4 years ago

again it would be more useful for the user if you could further parse the *.trace columns so that it is immediately obvious what line of user code the problem/address happens on. TODO create new columns problem.file.line, address.file.line or similar.

akhikolla commented 4 years ago

Using the problem.trace and address.trace column to store the problem file line, address file line

 code.line <- function(pattern){
    file.line.dt <- nc::capture_all_str(
      pattern,
      "==[0-9]+==","\\s*",
      trace=".*\n",
      ".*",
      Testharness)
    return(file.line.dt$trace)
    }

  rest <- gsub("==[0-9]+== Warning:.*?\\n","",messages.raw$rest)
  messages.parsed <- messages.raw[, {
    problems.dt <- nc::capture_all_str(
      rest,
      prefix(" "),
      problem="[^ \n].*",
      "\n",
      problem.trace=trace.pattern,
      prefix("  "),
      address=".*",
      "\n",
      address.trace=trace.pattern)
    problems.dt$problem.trace = code.line(problems.dt$problem.trace)
    problems.dt$address.trace = code.line(problems.dt$address.trace)
    data.table::data.table(
      problems=list(problems.dt))
  }, by=.(message.i)]

src file function and line number:

>  problems.dt$problem.trace = code.line(problems.dt$problem.trace)
> problems.dt$problem.trace
[1] "at 0x41FE2F: rcpp_use_after_free(int) (use_after_free.cpp:7)\n"
> problems.dt$address.trace = code.line(problems.dt$address.trace)
> problems.dt$address.trace 
[1] "by 0x41FE2A: rcpp_use_after_free(int) (use_after_free.cpp:6)\n"

Output:

message=1

inputs=alloc_size values: 1358703801

# A tibble: 1 x 4
  problem      problem.trace               address                   address.trace              
  <chr>        <chr>                       <chr>                     <chr>                      
1 Invalid rea… "at 0x41FE2F: rcpp_use_aft… Address 0x59e43068 is 40… "by 0x41FE2A: rcpp_use_aft…
tdhock commented 4 years ago

hi is this issue fixed?

akhikolla commented 4 years ago

It keeps throwing this error when I run the deepstate_display() function. I think the quantifier is unable to pick the lines from the log. I don't exactly understand what does this error mean ? can you please explain?

 Error in set(x, j = name, value = value) : 
  RHS of assignment to existing column 'problem.trace' is zero length but not NULL. If you intend to delete the column use NULL. Otherwise, the RHS must have length > 0; e.g., NA_integer_. If you are trying to change the column type to be an empty list column then, as with all column type changes, provide a full length RHS vector such as vector('list',nrow(DT)); i.e., 'plonk' in the new column. 
6.
set(x, j = name, value = value) 
5.
`$<-.data.table`(`*tmp*`, problem.trace, value = character(0)) 
4.
`$<-`(`*tmp*`, problem.trace, value = character(0)) 
3.
`[.data.table`(messages.raw, , {
    problems.dt <- nc::capture_all_str(rest, prefix(" "), problem = "[^ \n].*", 
        "\n", problem.trace = trace.pattern, prefix("  "), address = ".*", 
        "\n", address.trace = trace.pattern) ... 
2.
messages.raw[, {
    problems.dt <- nc::capture_all_str(rest, prefix(" "), problem = "[^ \n].*", 
        "\n", problem.trace = trace.pattern, prefix("  "), address = ".*", 
        "\n", address.trace = trace.pattern) ... 
1.
deepstate_displays("/home/akhila/Pictures/inst/testfiles/rcpp_use_after_free/rcpp_use_after_free_output/log_be80e0f43b5dbf4378a994a2024865c134114068/valgrind_log")

But when I run the individual dataframe generation code it works fine. It gives the output as expected.

deepstate_displays <- function(logfile){
  messages.raw <- nc::capture_all_str(
    logfile,
    "input starts\n",
    inputs="(?:.*\n)+?",
    "input ends\n",
    rest="(?:.+\n)+")
  messages.raw[, message.i := 1:.N]

  files.list<-nc::capture_all_str(logfile,"Command: ./",
                                  file.name=".*",
                                  "_DeepState_TestHarness")
  Testharness <- paste0("DeepState_Test_",basename(gsub("/inst/testfiles/.*","",logfile)),
                        "_deepstate_test_",files.list$file.name,"_test")

  prefix <- function(after){
    list("==[0-9]+==", after)
  }
  trace.pattern <- nc::quantifier(
    prefix("    "),
    "(?:at|by).*\n",
    "+")
  code.line <- function(pattern){
    file.line.dt <- nc::capture_all_str(
      pattern,
      "==[0-9]+==","\\s*",
      trace=".*\n",
      ".*",
      Testharness)
    return(file.line.dt$trace)
    }

  rest <- gsub("==[0-9]+== Warning:.*?\\n","",messages.raw$rest)
  if( length(rest) >= 1){ 
    messages.parsed <- messages.raw[, {
    problems.dt <- nc::capture_all_str(
      rest,
      prefix(" "),
      problem="[^ \n].*",
      "\n",
      problem.trace=trace.pattern,
      prefix("  "),
      address=".*",
      "\n",
      address.trace=trace.pattern)
    problems.dt$problem.trace = code.line(problems.dt$problem.trace)
    problems.dt$address.trace = code.line(problems.dt$address.trace)
    data.table::data.table(
      problems=list(problems.dt))
  }, by=.(message.i)]
    str(messages.parsed)
    for(message.i in 1:nrow(messages.parsed)){
      print(tibble::tibble(messages.parsed[["problems"]][[message.i]]))
    }
  }
tdhock commented 3 years ago

sorry I don't understand. if you want me to help can you please clarify with a Minimal Reproducible Example?

akhikolla commented 3 years ago

Resolved the issue and able to generate the log accordingly.

tdhock commented 3 years ago

ok to close this then?

akhikolla commented 3 years ago

Issue Resolved