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Segmentation fault in Rcpp::DataFrame::create when data is sufficiently long #226

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tmanka opened this issue Jan 14, 2015 · 6 comments
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Segmentation fault in Rcpp::DataFrame::create when data is sufficiently long #226

tmanka opened this issue Jan 14, 2015 · 6 comments
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@tmanka
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tmanka commented Jan 14, 2015

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

R isn't handling the dataframes created by Rcpp well and looks like crahes in its allocator.

I orginally added this bug to R but it was rejected by
Duncan Murdoch 2015-01-13 17:30:25 UTC

and Duncan said:

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

http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2012-January/003345.html

Please let me know if this is the right place to report this issue.

Thanks,
Ted

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=)
@eddelbuettel
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Jeebus. The stack trace is mostly useless.

Submit reproducible examples.

Better still, consult list archives, SO, other Rcpp documentation, ... and just create it as a very, very, very, very long list. Convert that to a data.frame in R.

The current Date.Frame class needs a rewrite. Volunteers welcome.

@tmanka
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tmanka commented Jan 14, 2015

Hi Dirk,

Let me work on that. Thank you for pointing me in the right direction.

Thanks,
Ted

@eddelbuettel
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No worries. The rcpp-devel list a great resource, please consider subscribing there and carrying the discussion over. It will get you more eyeballs.

@kevinushey
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As a workaround, consider building an Rcpp::List and manually turning it into a data.frame at the end, e.g.

// [[Rcpp::export]]
List list_as_df(List x) {
    R_xlen_t nrows = Rf_length(x[0]);
    x.attr("row.names") = IntegerVector::create(NA_INTEGER, nrows);
    x.attr("class") = "data.frame";
    return x;
}

A more robust implementation would handle edge cases (zero length list; list with differing number of rows; and so on...)

jackwasey pushed a commit to jackwasey/icd that referenced this issue Jan 21, 2015
return a Rcpp::List form of data.frame to work around RcppCore/Rcpp#226…
2b7990b 
… in comorbid.cpp
@coatless
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Probably should add this into the known issue section... I'm thinking about also mentioning at the same time that Rcpp::List can be used to get around the imposed 20 item limited DF ctor.

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This issue is stale (365 days without activity) and will be closed in 31 days unless new activity is seen. Please feel free to re-open it is still a concern, possibly with additional data.

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@eddelbuettel @coatless @thirdwing @kevinushey @tmanka