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dplyr::arrange causes R to crash #2308

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BillVenables opened this issue Dec 11, 2016 · 9 comments
Closed

dplyr::arrange causes R to crash #2308

BillVenables opened this issue Dec 11, 2016 · 9 comments

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@BillVenables
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BillVenables commented Dec 11, 2016 •
edited by krlmlr
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If you include in arrange() the name of a non-existent column on which to sort it can cause R itself to crash.
Here is an example.

> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_0.5.0

loaded via a namespace (and not attached):
[1] drat_0.1.2     magrittr_1.5   R6_2.2.0       assertthat_0.1 DBI_0.5-1     
[6] tools_3.3.2    parallel_3.3.2 tibble_1.2     Rcpp_0.12.8   
> d <- data.frame(a = runif(10))
> arrange(d, a, Dud)
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)
@r2evans
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r2evans commented Dec 14, 2016

FYI, this does not happen for me:

library(dplyr)
# Attaching package: 'dplyr'
# The following objects are masked from 'package:stats':
#     filter, lag
# The following objects are masked from 'package:base':
#     intersect, setdiff, setequal, union
d <- data.frame(a = runif(10))
arrange(d, a, Dud)
# Error in arrange_impl(.data, dots) : binding not found: 'Dud'
sessionInfo()
# R version 3.3.1 (2016-06-21)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 14393)
# locale:
# [1] LC_COLLATE=English_United States.1252 
# [2] LC_CTYPE=English_United States.1252   
# [3] LC_MONETARY=English_United States.1252
# [4] LC_NUMERIC=C                          
# [5] LC_TIME=English_United States.1252    
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# other attached packages:
# [1] dplyr_0.5.0.9000 r2_0.4.23       
# loaded via a namespace (and not attached):
#  [1] Rcpp_0.12.8     digest_0.6.10   rprojroot_1.1   assertthat_0.1 
#  [5] R6_2.2.0        DBI_0.5-13      backports_1.0.4 magrittr_1.5   
#  [9] evaluate_0.10   stringi_1.1.2   lazyeval_0.2.0  rmarkdown_1.2  
# [13] tools_3.3.1     stringr_1.1.0   compiler_3.3.1  htmltools_0.3.5
# [17] knitr_1.15.1    tibble_1.2

(I know the OP is on linux, R-3.3.2, and dplyr-0.5.0, just thought I'd add perspective.)

@krlmlr
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krlmlr commented Dec 15, 2016

Thanks. I couldn't replicate this on Linux either. But I see something strange happening in a vanilla R session with valgrind enabled:

==15136== Source and destination overlap in memcpy_chk(0x530d404, 0x530d400, 53)
==15136==    at 0x4C34467: __memcpy_chk (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==15136==    by 0x4F28951: memmove (string3.h:59)
==15136==    by 0x4F28951: R_ConciseTraceback.constprop.8 (errors.c:1384)
==15136==    by 0x4F29666: verrorcall_dflt (errors.c:684)
==15136==    by 0x4F2D60A: errorcall_dflt.constprop.6 (errors.c:712)
==15136==    by 0x4F2D67E: do_dfltStop (errors.c:1734)
==15136==    by 0x4F39DC0: bcEval (eval.c:5658)
==15136==    by 0x4F4499F: Rf_eval (eval.c:616)
==15136==    by 0x4F4661C: Rf_applyClosure (eval.c:1135)
==15136==    by 0x4F44B2C: Rf_eval (eval.c:732)
==15136==    by 0x23A548D1: dplyr_arrange_impl (RcppExports.cpp:67)
==15136==    by 0x4F09733: do_dotcall (dotcode.c:1251)
==15136==    by 0x4F44F5E: Rf_eval (eval.c:713)
==15136==

Could you please run:

R --vanilla --debugger=valgrind -e 'library(dplyr); d <- data.frame(a = runif(10)); arrange(d, a, Dud)'

@BillVenables
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BillVenables commented Dec 16, 2016 via email •
edited by krlmlr
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@krlmlr
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krlmlr commented Dec 16, 2016

Thanks. Could you please try Rcpp from GitHub and/or Rcpp 0.12.7 from the archives?

@BillVenables
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BillVenables commented Dec 16, 2016 via email

@krlmlr
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krlmlr commented Dec 16, 2016

Thanks. I assume all apt packages are up to date on your system? The next thing to try would be to install dplyr in a fresh R package library.

If that fails, could you please post valgrind output for 0.12.8.2? I'm still pretty sure it's an Rcpp issue, but the valgrind output will be helpful anyway.

@kevinushey
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Note that you likely need to re-install both Rcpp and dplyr; ie, you want to rebuild dplyr against the updated Rcpp sources.

@BillVenables
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BillVenables commented Dec 16, 2016 via email

@krlmlr
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krlmlr commented Dec 16, 2016

Thanks, to Bill for your patience, and to Kevin for the hint. I've brought R's lack of warnings here to R-devel, we'll see.

@krlmlr krlmlr mentioned this issue Dec 18, 2016
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@hadley hadley closed this as completed Jan 31, 2017
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5 participants
@hadley @krlmlr @kevinushey @r2evans @BillVenables