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Fatal Error #315

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ECDelmelle opened this issue Feb 1, 2023 · 21 comments
Closed

Fatal Error #315

ECDelmelle opened this issue Feb 1, 2023 · 21 comments

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@ECDelmelle
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ECDelmelle commented Feb 1, 2023 •
edited by rafapereirabr
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I am getting a 'fatal error' (with a scary picture of a bomb) that shuts down R studio when I try to run r5r -- either with the sample data or my own.

Here are the details:

r5r::r5r_sitrep()
$r5r_package_version
[1] ‘1.0.0’

$r5_jar_version
[1] "6.8"

$java_version
[1] "11.0.18"

$set_memory
[1] "-Xmx20G"

$session_info
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] dplyr_1.0.10      interp_1.1-3      ggplot2_3.3.6     data.table_1.14.2 r5r_1.0.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9         pillar_1.8.1       compiler_4.2.2     class_7.3-20       tools_4.2.2       
 [6] lifecycle_1.0.1    tibble_3.1.8       gtable_0.3.1       pkgconfig_2.0.3    rlang_1.0.5       
[11] DBI_1.1.3          cli_3.3.0          rstudioapi_0.14    rJava_1.0-6        e1071_1.7-11      
[16] withr_2.5.0        generics_0.1.3     vctrs_0.4.1        classInt_0.4-7     grid_4.2.2        
[21] tidyselect_1.1.2   glue_1.6.2         sf_1.0-9           R6_2.5.1           fansi_1.0.3       
[26] purrr_0.3.4        deldir_1.0-6       magrittr_2.0.3     scales_1.2.1       units_0.8-0       
[31] assertthat_0.2.1   colorspace_2.0-3   utf8_1.2.2         KernSmooth_2.23-20 proxy_0.4-27      
[36] munsell_0.5.0
@rafapereirabr
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Hi Elizabeth. Thanks for opening this issue. Everything looks fine with the installation from what I can see. Could you please restart your R session and run this code below?

options(java.parameters = '-Xmx4G')

library(r5r)

# build transport network
data_path <- system.file("extdata/poa", package = "r5r")
r5r_core <- setup_r5(data_path, overwrite = T)

# load origin/destination points
points <- read.csv(file.path(data_path, "poa_points_of_interest.csv"))

departure_datetime <- as.POSIXct(
  "13-05-2019 14:00:00",
  format = "%d-%m-%Y %H:%M:%S"
)

ttm <- travel_time_matrix(
  r5r_core,
  origins = points,
  destinations = points,
  mode = c("WALK", "TRANSIT"),
  departure_datetime = departure_datetime,
  max_trip_duration = 60, 
  progress = T
)

head(ttm)

This should give you this ouput:

#>          from_id               to_id travel_time_p50
#> 1: public_market       public_market               0
#> 2: public_market bus_central_station              13
#> 3: public_market    gasometer_museum              10
#> 4: public_market santa_casa_hospital              15
#> 5: public_market            townhall               3
#> 6: public_market     piratini_palace              17

Please, let me know if it works. If not, please paste the error message you get.

ps. I've never seen an error message with the picture of a bomb before, so now I'm really curious. If it happens again, could please share a printscreen of the picture ?

@ECDelmelle
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ECDelmelle commented Feb 1, 2023 •
edited by rafapereirabr
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That caused the bomb!
Screenshot 2023-02-01 at 9 54 02 AM

It also left me a note (error log) in my project folder with some error details that points to Java being the culprit. I can do some further digging unless something comes to your mind in dealing with this!

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000287af03d4, pid=54031, tid=259
#
# JRE version: Java(TM) SE Runtime Environment 18.9 (11.0.18+9) (build 11.0.18+9-LTS-195)
# Java VM: Java HotSpot(TM) 64-Bit Server VM 18.9 (11.0.18+9-LTS-195, mixed mode, tiered, compressed oops, g1 gc, bsd-aarch64)
# Problematic frame:
# J 535 c2 java.lang.StringLatin1.replace([BCC)Ljava/lang/String; java.base@11.0.18 (196 bytes) @ 0x0000000287af03d4 [0x0000000287af0300+0x00000000000000d4]
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   https://bugreport.java.com/bugreport/crash.jsp
#

@rafapereirabr
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Ah, that bomb! Did you install your jdk from here?

@ECDelmelle
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yes, but version 11 right? I had 19 installed, then got a different error, so I installed 11 and then had both and finally, got rid of 19. Then the bombs began...

@rafapereirabr
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Yes, it's version 11. I can only suspect that some important files must have been deleted when you unnistaled v. 19. Try reinstalling jdk 11 again and see it works

@ECDelmelle
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nothin' but bombs. I uninstalled and re-installed Java. No luck. Had a friend try with a slightly older Mac - we followed the identical steps and her's ended up running. So its not you! Will keep searching for a solution.

@rafapereirabr
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rafapereirabr commented Feb 3, 2023 •
edited
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Hey Elizabeth, any updates? I hope you've managed to disarm the bombs. I assume it is something to do with the Java installation

@ECDelmelle
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ECDelmelle commented Feb 3, 2023 via email

@rafapereirabr
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Gee.

Ok, try this.

  • Restart R
  • Open command prompt (I think it's called 'terminal' in MacOS) and run "ulimit -c unlimited"
  • Then try running the code of the example above

@ECDelmelle
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ECDelmelle commented Feb 5, 2023 via email

@rafapereirabr
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On a quick search, I came across this possible patch to the problem https://stackoverflow.com/questions/67849830/how-to-install-rjava-package-in-mac-with-m1-architecture

@rafapereirabr
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Hi @ECDelmelle . Have you had any success with this problem?

@charperflow
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Hi Rafapereirabr. I know I'm not the original poster, but I am also having the same Issue. I followed thelink above, and I was able to install jdk version 11 and load the rjava library just fine, however, I am still getting the bomb! I have attached the error report generated by the session in case that is helpful. Let me know if you need anymore information!
rsession-arm64-2023-02-24-153614.txt

@rafapereirabr
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Thanks for your message @charperflow. I see you also use MacBook with ARM cpu processor, so it serves as additional evidence this is a compatibility issue between jdk 11 and ARM cpu processors. I'm sorry there is nothing we can do from our side to help address this issue

@jleape
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jleape commented Aug 18, 2023

Had the same issue with my ARM mac. Would love to know if anyone figures out a work around!

@rafapereirabr rafapereirabr mentioned this issue Oct 2, 2023
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@hphoebe
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hphoebe commented Oct 6, 2023

For any future users with mac ARM processors facing this issue, I followed the steps from https://stackoverflow.com/questions/67849830/how-to-install-rjava-package-in-mac-with-m1-architecture (installing a x86_64 build of Java SDK version 11 from AdoptOpenJDK to be compatible with a x86_64 build of R) and was able to bypass the fatal error and run the example in this thread (albeit with some warnings during setup_r5).
terminal.txt

@rafapereirabr
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Thanks so much for sharing the solution you have found @hphoebe !

@higgicd higgicd mentioned this issue Oct 11, 2023
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@higgicd higgicd mentioned this issue Dec 4, 2023
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@higgicd
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higgicd commented Dec 4, 2023

I can confirm the sample code above now works fine with the dev version and Java SDK 21 on my M2 MacBook!

@rafapereirabr
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This is great. Thanks @higgicd .

@ECDelmelle , @hphoebe, @jleape and @charperflow. Could any of you please check wether the issue persists in your computer? See code below:

Clean install of dev version

utils::remove.packages('r5r')
devtools::install_github("ipeaGIT/r5r", subdir = "r-package")

Test code

options(java.parameters = '-Xmx4G')

library(r5r)

# build transport network
data_path <- system.file("extdata/poa", package = "r5r")
r5r_core <- setup_r5(data_path, overwrite = T)

# load origin/destination points
points <- read.csv(file.path(data_path, "poa_points_of_interest.csv"))

departure_datetime <- as.POSIXct(
  "13-05-2019 14:00:00",
  format = "%d-%m-%Y %H:%M:%S"
)

ttm <- travel_time_matrix(
  r5r_core,
  origins = points,
  destinations = points,
  mode = c("WALK", "TRANSIT"),
  departure_datetime = departure_datetime,
  max_trip_duration = 60, 
  progress = T
)

head(ttm)

@ECDelmelle
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ECDelmelle commented Dec 5, 2023 via email

@rafapereirabr
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Wonderful. Thanks for the feedback, @ECDelmelle . Closing this issue for now. We're planning a new update of r5r v2.0.0 soon and this issue should be fixed for good. Closing it for now.

@rafapereirabr rafapereirabr mentioned this issue Mar 1, 2024
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@rafapereirabr rafapereirabr mentioned this issue Mar 9, 2024
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@rafapereirabr rafapereirabr mentioned this issue Apr 8, 2024
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6 participants
@rafapereirabr @jleape @charperflow @higgicd @ECDelmelle @hphoebe