[BUGZILLA #16155] Segmentation fault in Rcpp::DataFrame::create when data is sufficiently long

[MichaelChirico]

We are encountering a crash that looks very similar to what was reported on the forum. Not sure if it ever made it to a bug.

Ours: (gdb) bt

0 0x00000039cd832925 in raise () from /lib64/libc.so.6

1 0x00000039cd834105 in abort () from /lib64/libc.so.6

2 0x000000000056f5af in handleSignals(int) ()

3

4 0x00007f3695a92239 in Rf_getCharCE () from /opt/vertica/R/lib/libR.so

5 0x00007f3695a9235d in Rf_translateChar () from /opt/vertica/R/lib/libR.so

6 0x00007f369598fc07 in vector2buff () from /opt/vertica/R/lib/libR.so

7 0x00007f369598f0ba in deparse2buff () from /opt/vertica/R/lib/libR.so

8 0x00007f369598cbe5 in deparse2 () from /opt/vertica/R/lib/libR.so

9 0x00007f369598bab3 in deparse1WithCutoff () from /opt/vertica/R/lib/libR.so

10 0x00007f369598bd23 in Rf_deparse1line () from /opt/vertica/R/lib/libR.so

11 0x00007f369595b6e4 in coerceVectorList () from /opt/vertica/R/lib/libR.so

12 0x00007f369595bd7d in Rf_coerceVector () from /opt/vertica/R/lib/libR.so

13 0x00007f369595c20f in ascommon () from /opt/vertica/R/lib/libR.so

14 0x00007f369595cbb4 in do_asvector () from /opt/vertica/R/lib/libR.so

15 0x00007f36959e2c44 in bcEval () from /opt/vertica/R/lib/libR.so

16 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

17 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

18 0x00007f3695a23dda in applyMethod () from /opt/vertica/R/lib/libR.so

19 0x00007f3695a24988 in Rf_usemethod () from /opt/vertica/R/lib/libR.so

20 0x00007f36959dd977 in Rf_DispatchOrEval () from /opt/vertica/R/lib/libR.so

21 0x00007f369595c666 in do_ascharacter () from /opt/vertica/R/lib/libR.so

22 0x00007f36959d88c9 in Rf_eval () from /opt/vertica/R/lib/libR.so

23 0x00007f3695a2b432 in do_paste () from /opt/vertica/R/lib/libR.so

24 0x00007f36959e2c44 in bcEval () from /opt/vertica/R/lib/libR.so

25 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

26 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

27 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

28 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

29 0x00007f36959d8401 in Rf_eval () from /opt/vertica/R/lib/libR.so

30 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

31 0x00007f36959d8492 in Rf_eval () from /opt/vertica/R/lib/libR.so

32 0x00007f36959e2093 in bcEval () from /opt/vertica/R/lib/libR.so

33 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

34 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

35 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

36 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

37 0x00007f36959ecaea in FORCE_PROMISE () from /opt/vertica/R/lib/libR.so

38 0x00007f36959ecc0a in getvar () from /opt/vertica/R/lib/libR.so

39 0x00007f36959e108d in bcEval () from /opt/vertica/R/lib/libR.so

40 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

41 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

42 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

43 0x00007f36959db10e in do_begin () from /opt/vertica/R/lib/libR.so

44 0x00007f36959d864c in Rf_eval () from /opt/vertica/R/lib/libR.so

45 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

46 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

47 0x00007f36959db10e in do_begin () from /opt/vertica/R/lib/libR.so

48 0x00007f36959d864c in Rf_eval () from /opt/vertica/R/lib/libR.so

49 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

50 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

51 0x00007f36959dce14 in do_eval () from /opt/vertica/R/lib/libR.so

52 0x00007f36959e2c44 in bcEval () from /opt/vertica/R/lib/libR.so

53 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

54 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

---Type to continue, or q to quit---

55 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

56 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

57 0x00007f36959ecaea in FORCE_PROMISE () from /opt/vertica/R/lib/libR.so

58 0x00007f36959ecc0a in getvar () from /opt/vertica/R/lib/libR.so

59 0x00007f36959e108d in bcEval () from /opt/vertica/R/lib/libR.so

60 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

61 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

62 0x00007f36959ecaea in FORCE_PROMISE () from /opt/vertica/R/lib/libR.so

63 0x00007f36959ecc0a in getvar () from /opt/vertica/R/lib/libR.so

64 0x00007f36959e108d in bcEval () from /opt/vertica/R/lib/libR.so

65 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

66 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

67 0x00007f36959ecaea in FORCE_PROMISE () from /opt/vertica/R/lib/libR.so

68 0x00007f36959ecc0a in getvar () from /opt/vertica/R/lib/libR.so

69 0x00007f36959e108d in bcEval () from /opt/vertica/R/lib/libR.so

70 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

71 0x00007f36959d80bc in forcePromise () from /opt/vertica/R/lib/libR.so

72 0x00007f36959ecaea in FORCE_PROMISE () from /opt/vertica/R/lib/libR.so

73 0x00007f36959ecc0a in getvar () from /opt/vertica/R/lib/libR.so

74 0x00007f36959e108d in bcEval () from /opt/vertica/R/lib/libR.so

75 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

76 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

77 0x00007f36959e2a1b in bcEval () from /opt/vertica/R/lib/libR.so

78 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

79 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

80 0x00007f36959e2a1b in bcEval () from /opt/vertica/R/lib/libR.so

81 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

82 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

83 0x00007f36959e2a1b in bcEval () from /opt/vertica/R/lib/libR.so

84 0x00007f36959d8275 in Rf_eval () from /opt/vertica/R/lib/libR.so

85 0x00007f36959d957c in Rf_applyClosure () from /opt/vertica/R/lib/libR.so

86 0x00007f36959d8964 in Rf_eval () from /opt/vertica/R/lib/libR.so

87 0x00007f3695054f85 in Rcpp::Evaluator::run(SEXPREC, SEXPREC) () from /opt/vertica/R/library/Rcpp/lib/libRcpp.so

88 0x00007f369505517d in Rcpp::Evaluator::run(SEXPREC*) () from /opt/vertica/R/library/Rcpp/lib/libRcpp.so

89 0x00007f3695055195 in Rcpp::internal::try_catch(SEXPREC*) () from /opt/vertica/R/library/Rcpp/lib/libRcpp.so

90 0x00000000005241df in Vertica::VerticaRInterface::processPartitionForR(RInside&, UDxSideProcessServerInterface&, Vertica::PartitionReader&, Vertica::PartitionWriter&, std::string const&, std::string const&) ()

91 0x00000000004d9b#0 0x00002b7f4a4b1594 in R_gc_internal (size_needed=0) at memory.c:1514

---

backtrace on the forum: http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2012-January/003335.html

0 0x00002b7f4a4b1594 in R_gc_internal (size_needed=0) at memory.c:1514

1 0x00002b7f4a4b34da in Rf_mkPROMISE (expr=0xf0dbf0f8, rho=0x904dab0) at memory.c:2165

2 0x00002b7f4a470e04 in Rf_promiseArgs (el=0xf0dbf0c0, rho=0x904dab0) at eval.c:1961

3 0x00002b7f4a479fc3 in Rf_eval (e=0xa3936a0, rho=0x904dab0) at eval.c:525

4 0x00002b7f4a47a90a in do_eval (call=0xa376c98, op=0x903d058, args=0xa38f2c0, rho=0xa38f100) at eval.c:2082

5 0x00002b7f4a4bc63e in do_internal (call=, op=, args=, env=0xa38f100) at names.c:1227

6 0x00002b7f4a47a139 in Rf_eval (e=0xa376c28, rho=0xa38f100) at eval.c:482

7 0x00002b7f4a47e678 in Rf_applyClosure (call=0xa393780, op=0xa3786e8, arglist=0xa3914b0, rho=0xa3ea258, suppliedenv=0x904dae8) at eval.c:838

8 0x00002b7f4a479feb in Rf_eval (e=0xa393780, rho=0xa3ea258) at eval.c:526

9 0x00002b7f4a47fbee in forcePromise (e=0xa3938d0) at eval.c:331

10 0x00002b7f4a47a373 in Rf_eval (e=0x907a5e8, rho=0xa3939b0) at eval.c:436

11 0x00002b7f4a47b8ad in do_return (call=0xa37cea0, op=, args=0x2b7f4a610f18, rho=0xa3939b0) at eval.c:1437

12 0x00002b7f4a47a139 in Rf_eval (e=0xa37cea0, rho=0xa3939b0) at eval.c:482

13 0x00002b7f4a47fbee in forcePromise (e=0xa3928a8) at eval.c:331

14 0x00002b7f4a47a373 in Rf_eval (e=0x907a5e8, rho=0xa390e58) at eval.c:436

15 0x00002b7f4a47b942 in do_begin (call=0xa37c848, op=0x9025d70, args=0x2b7f4a610f18, rho=0xa390e58) at eval.c:1420

16 0x00002b7f4a47a139 in Rf_eval (e=0xa37c848, rho=0xa390e58) at eval.c:482

17 0x00002b7f4a47e678 in Rf_applyClosure (call=0xa37cdf8, op=0xa393a20, arglist=0xa392918, rho=0xa3939b0, suppliedenv=0x904dae8) at eval.c:838

18 0x00002b7f4a479feb in Rf_eval (e=0xa37cdf8, rho=0xa3939b0) at eval.c:526

19 0x00002b7f4a47cbd7 in do_set (call=0xa37cd18, op=0x9025f68, args=0xa37cd50, rho=0xa3939b0) at eval.c:1722

20 0x00002b7f4a47a139 in Rf_eval (e=0xa37cd18, rho=0xa3939b0) at eval.c:482

21 0x00002b7f4a47b942 in do_begin (call=0xa3c84f8, op=0x9025d70, args=0x2b7f4a610f18, rho=0xa3939b0) at eval.c:1420

22 0x00002b7f4a47a139 in Rf_eval (e=0xa3c84f8, rho=0xa3939b0) at eval.c:482

23 0x00002b7f4a47e678 in Rf_applyClosure (call=0xa393828, op=0xa3e1940, arglist=0xa393908, rho=0xa3ea258, suppliedenv=0x904dae8) at eval.c:838

24 0x00002b7f4a479feb in Rf_eval (e=0xa393828, rho=0xa3ea258) at eval.c:526

25 0x00002b7f4f69affc in Rcpp::Evaluator::run (expr=0xa3936a0, env=0x904dab0) at Evaluator.cpp:36

26 0x00002b7f4f69b201 in Rcpp::Evaluator::run (expr=0xa3936a0) at Evaluator.cpp:58

27 0x00002b7f4f69b219 in Rcpp::internal::try_catch (expr=0xa3936a0) at Evaluator.cpp:78

28 0x00002b7f4f4522f8 in rcpp_hello_world (rlen=)

---

METADATA

• Bug author - Ted Manka
• Creation time - 2015-01-13 16:25:48 UTC
• Bugzilla link
• Status - CLOSED CONTRIBUTED PACKAGE
• Alias - None
• Component - Low-level
• Version - R 3.0.0
• Hardware - Other Linux
• Importance - P5 major
• Assignee - R-core
• URL -
• Modification time - 2015-01-14 15:18 UTC

[MichaelChirico]

Rcpp is a contributed package; this but list is for bugs in R. Please don't report contributed package bugs here.

---

METADATA

• Comment author - Duncan Murdoch
• Timestamp - 2015-01-13 17:30:25 UTC

[MichaelChirico]

I think R isn't handling the dataframes created by Rcpp well and looks like crahes in its allocator and that is why I opened it here. Please let me know if I should post it here or in RCPP?

Thanks, Ted

---

METADATA

• Comment author - Ted Manka
• Timestamp - 2015-01-14 15:14:34 UTC

[MichaelChirico]

Definitely sounds like an Rcpp issue. If it turns out to be an R issue, the Rcpp maintainers will let us know (by posting some example code that doesn't require the use of Rcpp.)

---

METADATA

• Comment author - Duncan Murdoch
• Timestamp - 2015-01-14 15:18:31 UTC