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xml2::xml_add_parent breaks under small stress. #803

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AleKoure opened this issue May 13, 2021 · 3 comments
Closed

xml2::xml_add_parent breaks under small stress. #803

AleKoure opened this issue May 13, 2021 · 3 comments

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@AleKoure
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AleKoure commented May 13, 2021 •
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System details

Output of sessioninfo::session_info()():

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
[1] xml2_1.3.2         plumber_1.1.0.9000

loaded via a namespace (and not attached):
 [1] compiler_4.0.4   magrittr_2.0.1   R6_2.5.0         later_1.2.0     
 [5] promises_1.2.0.1 tools_4.0.4      swagger_3.33.1   Rcpp_1.0.6      
 [9] remotes_2.3.0    stringi_1.6.1    jsonlite_1.7.2   webutils_1.1    
[13] lifecycle_1.0.0  rlang_0.4.11

Hello, I have run into the following issue.

If I add a parent node in xml2 and consecutively run many requests fast, then I fall into a memory issue.

library(plumber)
library(xml2)

#* Add parent to xml - destructive operation
#* @get /echo
function() {
  x <- read_xml("<fruits><apple color='red'></apple></fruits>")
  xml_add_parent(x, read_xml("<food></food>"))
  print(as.character(x))
}
1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
free(): invalid pointer
[637681:637681:20210513,173356.782994:ERROR process_memory_range.cc:86] read out of range
[637681:637681:20210513,173356.783091:ERROR elf_image_reader.cc:558] missing nul-terminator
[637681:637681:20210513,173356.783374:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.786279:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.786398:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.786504:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.786930:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.787179:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.787328:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.788727:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.788860:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.794399:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.794554:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.794684:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.794806:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.794935:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795055:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795189:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795317:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795594:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795744:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637681:20210513,173356.795865:ERROR elf_dynamic_array_reader.h:61] tag not found
[637681:637682:20210513,173356.804233:ERROR directory_reader_posix.cc:42] opendir: No such file or directory (2)

I can work around this by using xml_add_child and 2-3 more lines of code for now, but it looks like a bug for plumber and destructive xml operators.

Thank you for maintaining plumber.
@meztez
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meztez commented May 13, 2021

I believe you are seeing an RStudio error:

rstudio/rstudio#7310

Are you able to reproduce without RStudio?

@AleKoure
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AleKoure commented May 13, 2021 •
edited
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Yes I got it from a docker container initially I use in a remote VM. Just used Rstudio to make a minimal example.

Reproducing from a terminal in my local machine.

  • First I save the following in a file named plumbMe.R
library(plumber)
library(xml2)

#* Add parent to xml - destructive operation
#* @get /echo
function() {
  x <- read_xml("<fruits><apple color='red'></apple></fruits>")
  xml_add_parent(x, read_xml("<food></food>"))
  print(as.character(x))
}
  • Then I navigate to swagger and press repeatedly execute:
R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> plum <- plumber::plumb("plumbMe.R")
> plumber::pr_run(plum)
Running plumber API at http://127.0.0.1:4463
Running swagger Docs at http://127.0.0.1:4463/__docs__/
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<food>\n  <fruits>\n    <apple color=\"red\"/>\n  </fruits>\n</food>\n"

 *** caught segfault ***
address 0x556390000000, cause 'memory not mapped'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Things work ok until I 'speed up' clicking. I get this behavior in the remote server as well.
Non destructive operations like xml_replace and xml_add_child work fine.

@AleKoure
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AleKoure commented May 14, 2021 •
edited
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Actually, it looks like an xml2 error

library(plumber)
library(xml2)

xx <- function() {
  x <- read_xml("<fruits><apple color='red'></apple></fruits>")
  xml_add_parent(x, read_xml("<food></food>"))
  print(as.character(x))
}

for(i in 1:1000)xx()

produces the same error.

related xml2 issue

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@AleKoure @meztez