R crashing intermitently #115

aphalo · 2018-09-28T11:32:23Z

Summary

When building the vignettes of 'ggspectra' R crashes intermittently in chunks which use geom_label_repel with long vectors of labels. These same examples have been working well for several versions of 'ggspectra'.

Minimal code example

I have no example yet that consistently triggers this problem. Could this problem be the result of a memory leak?

Question

Is this a known problem?

Version information

Here is the output from sessionInfo() in my R session:

R version 3.5.1 Patched (2018-09-25 r75362)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] bindrcpp_0.2.2              knitr_1.20                  ggrepel_0.8.0              
[4] ggspectra_0.2.5-1           photobiologyWavebands_0.4.2 photobiology_0.9.24        
[7] scales_1.0.0                ggplot2_3.0.0              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18     pillar_1.3.0     compiler_3.5.1   plyr_1.8.4       bindr_0.1.1     
 [6] tools_3.5.1      digest_0.6.17    packrat_0.4.9-3  evaluate_0.11    lubridate_1.7.4 
[11] tibble_1.4.2     gtable_0.2.0     pkgconfig_2.0.2  rlang_0.2.2      rstudioapi_0.7  
[16] yaml_2.2.0       withr_2.1.2      dplyr_0.7.6      stringr_1.3.1    rprojroot_1.3-2 
[21] grid_3.5.1       tidyselect_0.2.4 glue_1.3.0       R6_2.2.2         rmarkdown_1.10  
[26] purrr_0.2.5      splus2R_1.2-2    magrittr_1.5     backports_1.1.2  htmltools_0.3.6 
[31] assertthat_0.2.0 colorspace_1.3-2 labeling_0.3     stringi_1.2.4    lazyeval_0.2.1  
[36] munsell_0.5.0    crayon_1.3.4    
--

slowkow · 2018-09-28T13:40:31Z

Is there any error message printed to the console?

…

On Fri, Sep 28, 2018, 7:32 AM Pedro Aphalo ***@***.***> wrote: Summary When building the vignettes of 'ggspectra' R crashes intermittently in chunks which use geom_label_repel with long vectors of labels. These same examples have been working well for several versions of 'ggspectra'. Minimal code example I have no example yet that consistently triggers this problem. Could this problem be the result of a memory leak? Question Is this a known problem? Suggested solution I will investigate this in detail next week, unless this is a known issue. Version information Here is the output from sessionInfo() in my R session: R version 3.5.1 Patched (2018-09-25 r75362) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] bindrcpp_0.2.2 knitr_1.20 ggrepel_0.8.0 [4] ggspectra_0.2.5-1 photobiologyWavebands_0.4.2 photobiology_0.9.24 [7] scales_1.0.0 ggplot2_3.0.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.18 pillar_1.3.0 compiler_3.5.1 plyr_1.8.4 bindr_0.1.1 [6] tools_3.5.1 digest_0.6.17 packrat_0.4.9-3 evaluate_0.11 lubridate_1.7.4 [11] tibble_1.4.2 gtable_0.2.0 pkgconfig_2.0.2 rlang_0.2.2 rstudioapi_0.7 [16] yaml_2.2.0 withr_2.1.2 dplyr_0.7.6 stringr_1.3.1 rprojroot_1.3-2 [21] grid_3.5.1 tidyselect_0.2.4 glue_1.3.0 R6_2.2.2 rmarkdown_1.10 [26] purrr_0.2.5 splus2R_1.2-2 magrittr_1.5 backports_1.1.2 htmltools_0.3.6 [31] assertthat_0.2.0 colorspace_1.3-2 labeling_0.3 stringi_1.2.4 lazyeval_0.2.1 [36] munsell_0.5.0 crayon_1.3.4 -- — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#115>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAMzMp5ifwK6OnrmlndiW-h45-bKNuxXks5ufgjIgaJpZM4W-Vvu> .

aphalo · 2018-09-28T13:49:48Z

No, just R has crashed when knitting in RStudio, and system error when building the package or checking it, but only occasionally. However, my laptop has been misbehaving lately, so if this problem has not been earlier reported I think I will investigate by myself and let you know my progress sometime next week. I have yet to see the problem in Winbuilder...

aphalo · 2018-10-03T11:01:04Z

Problem seems to be in my own package. Sorry about the false alarm!
I am closing the issue because of this.

aphalo · 2018-10-06T14:03:43Z

@slowkow I have now found a way of reproducing the R crashes. Seems to be a memory corruption or something related. Long vectors of labels, like those we discussed about earlier as a way of avoiding overlap with data points by setting labels to "", no longer work in 'ggrepel' 0.8.0. In some cases when the data is not so big, the crash of R may happen after the plot is printed on a subsequent call to a different R function.

# test for bug in ggrepel/ggplot2
library(ggplot2)
library(ggrepel)

# sometimes works, usually R crashes
n = 1000L
my.data <- data.frame(x = runif(n), y = runif(n),
                      my.label = c(rep("", n/100 - 1), "abcd"))

# ggplot(my.data, aes(x, y, label = my.label)) +
#  geom_label()

ggplot(my.data, aes(x, y, label = my.label)) +
  geom_label_repel()

# never works, R crashes

n = 10000L
my.data <- data.frame(x = runif(n), y = runif(n),
                      my.label = c(rep("", n/1000 - 1), "abcd"))

# ggplot(my.data, aes(x, y, label = my.label)) +
#  geom_label()

ggplot(my.data, aes(x, y, label = my.label)) +
  geom_label_repel()

The system data is:

- Session info -------------------------------------------------------
 setting  value                                      
 version  R version 3.5.1 Patched (2018-09-25 r75362)
 os       Windows >= 8 x64                           
 system   x86_64, mingw32                            
 ui       RStudio                                    
 language (EN)                                       
 collate  English_United Kingdom.1252                
 ctype    English_United Kingdom.1252                
 tz       Europe/Helsinki                            
 date     2018-10-06                                 

- Packages -----------------------------------------------------------
 package     * version date       lib source                          
 assertthat    0.2.0   2017-04-11 [1] CRAN (R 3.5.0)                  
 bindr         0.1.1   2018-03-13 [1] CRAN (R 3.5.0)                  
 bindrcpp      0.2.2   2018-03-29 [1] CRAN (R 3.5.0)                  
 cli           1.0.1   2018-09-25 [1] CRAN (R 3.5.1)                  
 colorspace    1.3-2   2016-12-14 [1] CRAN (R 3.5.0)                  
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.5.0)                  
 dplyr         0.7.6   2018-06-29 [1] CRAN (R 3.5.0)                  
 ggplot2     * 3.0.0   2018-07-03 [1] CRAN (R 3.5.1)                  
 ggrepel     * 0.8.0   2018-05-09 [1] CRAN (R 3.5.1)                  
 glue          1.3.0   2018-07-17 [1] CRAN (R 3.5.1)                  
 gtable        0.2.0   2016-02-26 [1] CRAN (R 3.5.0)                  
 lazyeval      0.2.1   2017-10-29 [1] CRAN (R 3.5.0)                  
 magrittr      1.5     2014-11-22 [1] CRAN (R 3.5.0)                  
 munsell       0.5.0   2018-06-12 [1] CRAN (R 3.5.0)                  
 packrat       0.4.9-3 2018-06-01 [1] CRAN (R 3.5.0)                  
 pillar        1.3.0   2018-07-14 [1] CRAN (R 3.5.1)                  
 pkgconfig     2.0.2   2018-08-16 [1] CRAN (R 3.5.1)                  
 plyr          1.8.4   2016-06-08 [1] CRAN (R 3.5.0)                  
 purrr         0.2.5   2018-05-29 [1] CRAN (R 3.5.0)                  
 R6            2.3.0   2018-10-04 [1] CRAN (R 3.5.1)                  
 Rcpp          0.12.19 2018-10-01 [1] CRAN (R 3.5.1)                  
 rlang         0.2.2   2018-08-16 [1] CRAN (R 3.5.1)                  
 rstudioapi    0.8     2018-10-02 [1] CRAN (R 3.5.1)                  
 scales        1.0.0   2018-08-09 [1] CRAN (R 3.5.1)                  
 sessioninfo   1.1.0   2018-09-25 [1] CRAN (R 3.5.1)                  
 tibble        1.4.2   2018-01-22 [1] CRAN (R 3.5.0)                  
 tidyselect    0.2.4   2018-02-26 [1] CRAN (R 3.5.0)                  
 withr         2.1.2   2018-08-27 [1] Github (jimhester/withr@8b9cee2)

[1] C:/Users/aphalo/Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.1patched/library

Hope this helps.

slowkow · 2018-10-06T15:40:52Z

Thanks for sharing an example. It does not crash R on my system.

At this point, my best guess is that the problem might be revealed by comparing the compiler output for the C++ code on Windows and macOS.

You might consider recompiling the code by yourself on your own machine instead of running the compiled code from CRAN.

My system:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

On my MacBook, I can run the first example with 1000 points and 100 labels:

   user  system elapsed
  3.245   0.133   3.603

Here is the second plot:

   user  system elapsed
151.761   1.648 157.032

aphalo · 2018-10-06T17:08:09Z

I installed 'ggrepel' from sources from CRAN, and this did not solve the problem.
There seems to be some new tests in CRAN, and one could explain the problem, I think.
https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/ggrepel/00check.log
I mean the "heap-buffer-overflow" near the end of the file.

slowkow · 2018-10-06T18:41:18Z

Pedro, thank you! I never noticed that log, but it should help to figure this out.

I found a nice blog post by Brian J. Knaus that should help get us started:

https://knausb.github.io/2017/06/cran-memory-error/

Since your system is crashing, I think you have a good chance to find the bug if you're able and willing. Please feel free to go ahead and hunt for the bug. I'll be very grateful if you can fix it!

My system is not crashing, so it looks like there is a lot of work ahead to find the bug:

Find a system that does crash with your provided code example.
Setup an environment with the address sanitizer (ASAN).
Reproduce the error log from CRAN.
Run R in a debugger.
Figure out which code is causing trouble.

I'd like to ask for help on this issue. If anyone wants to try to fix this, I would greatly appreciate your help. I'm not sure if I can fix this any time soon.

aphalo · 2018-10-06T19:07:40Z

Must be a new type of log. I saw it for the first time only today. I am very busy at the moment with teaching and manuscripts about to be submitted. I'll give a go at continuing the debugging next weekend, unless I find some free time tomorrow. If you have any code that needs to be quickly tested, I can handle that a lot faster.

slowkow · 2018-10-06T19:12:39Z

OK, don't worry about it for now. I will spend some time and see if I make any progress.

Just browsing around, I found some nice new packages and websites that should make this easier.

For example, I think I should be able to test the package with ASAN just like this:

# In the ggrepel directory.

install.packages("rhub")
library(rhub)

# Validate your email address and get an access token.
validate_email()

# Send the tar.gz file to https://builder.r-hub.io
# Check it for errors with ASAN
check_with_sanitizers()

aphalo · 2018-10-06T19:50:52Z

I had not noticed that 'rhub' now has check_with_sanitizers(). I have used rhub from time to time but sometimes some packages are missing. Otherwise works well.

slowkow · 2018-10-06T20:29:54Z

My first attempt did not reproduce the CRAN error:

https://builder.r-hub.io/status/ggrepel_0.8.0.tar.gz-9779cd78b03c425fa366849cf09189d5#L2368

I tried again with this command:

# First, download the source package for ggrepel from CRAN.

# Test it.
check_with_sanitizers(
  path = "ggrepel_0.8.0.tar.gz",
  check_args = '--as-cran --no-stop-on-test-error'
)

But I don't think it actually executed the same code as the CRAN log:

https://builder.r-hub.io/status/ggrepel_0.8.0.tar.gz-198f9a4fd10e41c6999754cddbea83b8

I'm not sure where to go from here... any tips would be helpful!

aphalo · 2018-10-07T08:41:19Z

I looked at the commits and you haven't made many edits to the C++ code recently. The only further insight is that the crash happens when the figure is printed rather than when the ggplot2 object is constructed.

aphalo · 2018-10-28T22:09:37Z

@slowkow I have just updated to 'ggplot2' 3.1.0 (and 'rlang' and 'tidyr') and I can no longer reproduce the error. Hopefully this is the end of this problem. I am not closing this issue yet, as probably some additional testing would be a good idea.

aphalo · 2018-10-28T22:29:43Z

@slowkow I was too fast, after a few successful checks the problem started to repeat, and was not cured by restarting Windows. So, once again, crashes are reproducible... part of the time.

slowkow · 2018-10-29T00:07:44Z

I'm still interested to fix the bug in your linked report. (I copied it here to make sure I can read it later.)

Unfortunately, I don't have time right now to setup my development environment with the necessary tools to track it down.

Thanks again for reporting this! Eventually this will need to get fixed. I hope it doesn't slow you down too much. Sorry I can't offer more support right now.

ERROR: AddressSanitizer: heap-buffer-overflow

* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel.Rcheck’ * using R Under development (unstable) (2018-10-22 r75478) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ggrepel/DESCRIPTION’ ... OK * this is package ‘ggrepel’ version ‘0.8.0’ * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘ggrepel’ can be installed ... [78s/85s] OK * checking package directory ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [11s/12s] OK * checking tests ... [30s/30s] OK Running ‘testthat.R’ [29s/29s] * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [10s/11s] WARNING Error in re-building vignettes: ... Warning in hook_png(before, options, envir, "pngquant", function(x) { : cannot find pngquant; please install and put it in PATH ================================================================= ==37138==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x608000002a00 at pc 0x7f3635a98931 bp 0x7ffe80159f50 sp 0x7ffe80159f40 READ of size 32 at 0x608000002a00 thread T0 #0 0x7f3635a98930 in repel_boxes(Rcpp::Matrix<14, Rcpp::PreserveStorage>, double, double, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, int, std::__cxx11::basic_string, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel/src/repel_boxes.cpp:631 #1 0x7f3635a2bcaa in _ggrepel_repel_boxes /data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel/src/RcppExports.cpp:87 #2 0x56773a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:617 #3 0x570fcb in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252 #4 0x61c427 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6769 #5 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #6 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #7 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #8 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #9 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #10 0x6e316a in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:433 #11 0x6e3ed6 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #12 0x6e4727 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:562 #13 0x618ca2 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6789 #14 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #15 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #16 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #17 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #18 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #19 0x641cf3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:743 #20 0x5bc361 in do_recordGraphics /data/gannet/ripley/R/svn/R-devel/src/main/engine.c:3107 #21 0x61c427 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6769 #22 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #23 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #24 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #25 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #26 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #27 0x6e316a in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:433 #28 0x6e3b58 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:469 #29 0x6e4727 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:562 #30 0x618ca2 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6789 #31 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #32 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #33 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #34 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #35 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #36 0x641cf3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:743 #37 0x5bc361 in do_recordGraphics /data/gannet/ripley/R/svn/R-devel/src/main/engine.c:3107 #38 0x61c427 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6769 #39 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #40 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #41 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #42 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #43 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #44 0x6e316a in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:433 #45 0x6e3b58 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:469 #46 0x6e4727 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:562 #47 0x618ca2 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6789 #48 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #49 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #50 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #51 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #52 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #53 0x641cf3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:743 #54 0x5bc361 in do_recordGraphics /data/gannet/ripley/R/svn/R-devel/src/main/engine.c:3107 #55 0x61c427 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6769 #56 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #57 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #58 0x6208f7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6737 #59 0x6417ef in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620 #60 0x646945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1780 #61 0x6e316a in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:433 #62 0x6e3b58 in Rf_usemethod 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/data/gannet/ripley/R/svn/R-devel/src/main/main.c:260 #219 0x6b88d0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:310 #220 0x6b8a04 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1084 #221 0x417b88 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #222 0x7f364b26711a in __libc_start_main (/lib64/libc.so.6+0x2311a) #223 0x41a2b9 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41a2b9)

0x608000002a00 is located 0 bytes to the right of 96-byte region [0x6080000029a0,0x608000002a00)
allocated by thread T0 here:
#0 0x7f364eef9870 in operator new(unsigned long) (/lib64/libasan.so.5+0xf0870)
#1 0x7f3635a8f823 in __gnu_cxx::new_allocator::allocate(unsigned long, void const*) /usr/include/c++/8/ext/new_allocator.h:111
#2 0x7f3635a8f823 in std::allocator_traits<std::allocator >::allocate(std::allocator&, unsigned long) /usr/include/c++/8/bits/alloc_traits.h:436
#3 0x7f3635a8f823 in std::_Vector_base<Box, std::allocator >::_M_allocate(unsigned long) /usr/include/c++/8/bits/stl_vector.h:296
#4 0x7f3635a8f823 in std::_Vector_base<Box, std::allocator >::_M_create_storage(unsigned long) /usr/include/c++/8/bits/stl_vector.h:311
#5 0x7f3635a8f823 in std::_Vector_base<Box, std::allocator >::_Vector_base(unsigned long, std::allocator const&) /usr/include/c++/8/bits/stl_vector.h:260
#6 0x7f3635a8f823 in std::vector<Box, std::allocator >::vector(unsigned long, std::allocator const&) /usr/include/c++/8/bits/stl_vector.h:416
#7 0x7f3635a8f823 in repel_boxes(Rcpp::Matrix<14, Rcpp::PreserveStorage>, double, double, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, int, std::__cxx11::basic_string<char, std::char_traits, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel/src/repel_boxes.cpp:581
#8 0x7f3635a2bcaa in _ggrepel_repel_boxes /data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel/src/RcppExports.cpp:87
#9 0x56773a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:617

SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/ggrepel/src/repel_boxes.cpp:631 in repel_boxes(Rcpp::Matrix<14, Rcpp::PreserveStorage>, double, double, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, int, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)
Shadow bytes around the buggy address:
0x0c107fff84f0: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c107fff8500: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c107fff8510: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c107fff8520: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
0x0c107fff8530: fa fa fa fa 00 00 00 00 00 00 00 00 00 00 00 00
=>0x0c107fff8540:[fa]fa fa fa fd fd fd fd fd fd fd fd fd fd fd fa
0x0c107fff8550: fa fa fa fa fd fd fd fd fd fd fd fd fd fd fd fd
0x0c107fff8560: fa fa fa fa fd fd fd fd fd fd fd fd fd fd fd fa
0x0c107fff8570: fa fa fa fa fd fd fd fd fd fd fd fd fd fd fd fd
0x0c107fff8580: fa fa fa fa fd fd fd fd fd fd fd fd fd fd fd fd
0x0c107fff8590: fa fa fa fa fd fd fd fd fd fd fd fd fd fd fd fd
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
==37138==ABORTING

DONE
Status: 1 WARNING

HughParsonage · 2018-12-09T12:11:01Z

Just some observations. My C++ is not good enough to detect buffer overflows just by reading, so probably red herrings:

The line

ratios[i] = (TextBoxes[i].y2 - TextBoxes[i].y1)
  / (TextBoxes[i].x2 - TextBoxes[i].x1);
original_centroids[i] = centroid(TextBoxes[i], hjust[i], vjust[i]);

a. Are zero-width labels going to cause divide-by-zero problems in ratios[i]. (Also where is ratios used?)

b. Are we sure that hjust[i] and vjust[i] are safe here?

m20ty · 2019-02-14T12:54:40Z

Has there been any progress on this issue? I have experienced the same problem (on Windows) - R crashes intermittently when trying to print figures which use ggrepel with long vectors of labels. I use ggrepel a lot - it's very useful and saves me a lot of time - so I'm following this issue with interest! I definitely haven't the programming knowledge to help, unfortunately.

slowkow · 2019-02-14T13:48:36Z

@m20ty Sorry to hear that, Mike. No progress yet. Thanks for letting us know that you have the same problem. That increases my confidence that there is a bug in the C++ code. Still very weird that I never see this on macOS.

For those of you experiencing this issue, could I please ask you to try compiling the source code? Try installing ggrepel like this:

install.packages("ggrepel", type = "source")

Then close your R session and start a fresh one.

Does this issue continue? Does it go away?

HughParsonage · 2019-02-14T13:50:33Z

Confirm that even compiling from source on Windows reproduces the issue.

…

On Fri, 15 Feb 2019 at 12:48 am, Kamil Slowikowski ***@***.***> wrote: @m20ty <https://github.com/m20ty> Sorry to hear that, Mike. No progress yet. Thanks for letting us know that you have the same problem. That increases my confidence that there is a bug in the C++ code. Still very weird that I never see this on macOS. For those of you experiencing this issue, could I please ask you to try compiling the source code? Try installing ggrepel like this: install.packages("ggrepel", type = "source") Then close your R session and start a fresh one. Does this issue continue? Does it go away? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#115 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHvGDIe2Ukb5_zfYnlmx8Cp8UZ2odSleks5vNWk1gaJpZM4W-Vvu> .

HughParsonage · 2019-02-14T13:51:32Z

Sorry — I meant after compiling from source I can still reproduce, not that I can reproduce the memory fault simply by installing. On Fri, 15 Feb 2019 at 12:50 am, HughParsonage <notifications@github.com> wrote:

…

Confirm that even compiling from source on Windows reproduces the issue. On Fri, 15 Feb 2019 at 12:48 am, Kamil Slowikowski < ***@***.***> wrote: > @m20ty <https://github.com/m20ty> Sorry to hear that, Mike. No progress > yet. Thanks for letting us know that you have the same problem. That > increases my confidence that there is a bug in the C++ code. Still very > weird that I never see this on macOS. > > For those of you experiencing this issue, could I please ask you to try > compiling the source code? Try installing ggrepel like this: > > install.packages("ggrepel", type = "source") > > Then close your R session and start a fresh one. > > Does this issue continue? Does it go away? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#115 (comment)>, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AHvGDIe2Ukb5_zfYnlmx8Cp8UZ2odSleks5vNWk1gaJpZM4W-Vvu > > . > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#115 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHvGDHNzo2L89vFpRg2hF4vGtFsJ-uEWks5vNWmqgaJpZM4W-Vvu> .

m20ty · 2019-02-14T15:20:35Z

I can also reproduce the issue after installing from source on Windows.

slowkow · 2019-02-22T14:41:51Z

Kurt Hornik from CRAN says we need to fix this by 2019-03-08 to safely retain ggrepel package on CRAN.

If anyone would like to help contribute by fixing this bug, many ggrepel users would be very grateful for your help.

Here are the log files that show the errors:

https://cran.r-project.org/web/checks/check_results_ggrepel.html

In particular, have a look at one of these 2 files:

https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/ggrepel/00check.log

https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-ASAN/ggrepel/00check.log

slowkow · 2019-02-24T03:33:00Z

@m20ty @HughParsonage @aphalo

Could you try the new code I just pushed? I think I fixed the heap buffer overflow error.

HughParsonage · 2019-02-24T03:37:13Z

Can confirm the problem is fixed. Ran the reprex above without issue. Thank you!

aphalo · 2019-02-24T17:10:54Z

@slowkow I can also confirm that the vignettes of 'ggspectra' no longer crash R under Windows 10. i.e. the bug I reported when I opened this issue seems to have been solved.

slowkow · 2019-02-24T17:56:19Z

@HughParsonage @aphalo I'm very happy to hear that.

I'm sorry for all the crashes. I know it can be frustrating and disruptive to your work, and I apologize for causing this issue. I really hope I didn't disrupt your work too badly. Thanks for your patience!

Since this fix is important, I will try to push a new release of ggrepel to CRAN as soon as possible.

aphalo closed this Oct 3, 2018

aphalo reopened this Oct 6, 2018

slowkow added bug help wanted labels Oct 6, 2018

slowkow closed this in cad83bb Feb 24, 2019

slowkow removed the help wanted label Feb 24, 2019

slowkow / ggrepel

R crashing intermitently #115

R crashing intermitently #115

aphalo commented Sep 28, 2018

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R crashing intermitently #115

R crashing intermitently #115

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aphalo commented Sep 28, 2018

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aphalo commented Oct 6, 2018 •

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