travel_time_matrix error: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException. GTFS or r5r issue?

[hugocbustamante]

Brief description of the problem:

Hello there! I've tried to calculate travel time matrix for Transit mode using GTFS data of The Netherlands and I get the following error:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
In addition: Warning messages:
1: In assign_points_input(origins, "origins") :
'origins$id' forcefully cast to character.
2: In assign_points_input(destinations, "destinations") :
'destinations$id' forcefully cast to character.

I've read other similar issues here and they seem to mostly relate to GTFS problems. However, I was able to calculate the travel time matrix with r5r version "1.1.0" and java jdk-11. Thus, I'm wondering if my problem is really in the GTFS side. I tried multiple GTFS files from NL but none of them seem to work with the latest r5r version.

Data files:
The files I used are too large to attach, but you can find them in:

• GTFS: https://transitfeeds.com/p/ov/814/20230305
• osm: netherlands-230101.osm.pbf

Thanks in advance for the help.

Reproducible example here

library(r5r)
options(java.parameters = '-Xmx16G')

library(bit64)
library(tibble)

r5r_core <- setup_r5(data_path = path, verbose = FALSE, overwrite = TRUE)

All_Existing_Nodes <- tibble(
  id = as.integer64(c(1, 2, 3, 4, 5)),   # Integer64 column
  lon = c(3.848480, 3.850004, 3.854776, 4.093418, 4.091302),   # Numeric longitude values
  lat = c(51.75870, 51.76108, 51.75399, 51.75992, 51.79841)   # Numeric latitude values
)

transit_travel_matrix_2023<-travel_time_matrix(
  r5r_core = r5r_core,
  origins = All_Existing_Nodes,
  destinations = All_Existing_Nodes,
  mode = "TRANSIT",
  mode_egress = "WALK",
  departure_datetime = as.POSIXct("28-03-2023 08:00:00", format = "%d-%m-%Y %H:%M:%S"),
  time_window = 30L,
  percentiles = c(1L,20L,50L,80L),  
  max_trip_duration = 60L,
  walk_speed = 3.6,
  max_rides = 3,
  n_threads = Inf,
  verbose = F,
  progress = T,
  output_dir = NULL
)

Situation report here

$r5r_package_version
[1] ‘2.0’

$r5_jar_version
[1] "7.1"

$java_version
[1] "21.0.4"

$set_memory
[1] "-Xmx16G"

$session_info
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
[1] rJava_1.0-11    RPostgres_1.4.6

loaded via a namespace (and not attached):
 [1] lubridate_1.9.3   bit_4.0.5         blob_1.2.4        r5r_2.0           pkgconfig_2.0.3   timechange_0.3.0 
 [7] generics_0.1.3    bit64_4.0.5       lifecycle_1.0.4   cli_3.6.2         vctrs_0.6.5       DBI_1.2.3        
[13] data.table_1.15.4 compiler_4.3.3    rstudioapi_0.16.0 tools_4.3.3       hms_1.1.3         rlang_1.1.3   

[rafapereirabr]

Thanks @hugocbustamante for opening this issue. I was able to reproduce the error. The code works fine when calcuating a travel time matrix for "WALK" mode, but it throws that error with "TRANSIT".

When you say you were able to calcuate a travel time matrix for "TRANSIT" using r5r version "1.1.0", were you using this exact same GTFS data ?

[hugocbustamante]

Hi @rafapereirabr, thanks for your quick reply. Yes, I was able to calculate it with the exact same GTFS data.

[rafapereirabr]

Hmm. That's strange. We'll have to look into this, but we need someone who knows Java because the source of the problem would probably be in the Java side of r5r. @hugocbustamante , would you have any experience with Java?

[hugocbustamante]

Unfortunately not, @rafapereirabr :(

[robrik87]

I have the same issue but with GTFS-data from Sweden.

[rafapereirabr]

Have you tried diagonosing the quality of your GTFS feeds ? If not, I would strongly recommend to do so using the {gtfstools} package. You can install the dev version directly from Github while we're working to put it back on CRAN

[erik-toi]

I have a similar issue with data from Norway. I have tried validating the GTFS and find several errors. Do you have any tips on how to fix GTFS feeds?

[robrik87]

I have a similar issue with data from Norway. I have tried validating the GTFS and find several errors. Do you have any tips on how to fix GTFS feeds?

@erik-toi @rafapereirabr

I found a solution that works! On the website busmaps.com, there are GTFS files that have been improved in terms of codes and structure. When I used their GTFS file for Sweden, the program ran successfully, with the exception that I needed to change route_type 1501 to 3.

Unfortunately, I don't know exactly what it is in their file that makes it work. I tried to compare it with my original file (which originally comes from the same source), but I can't quite figure out what the difference is. If anyone can help identify the exact problem, I'd be very grateful.

Anyway, busmaps.com's GTFS files work as a solution, and I'm very thankful that they provide them openly. However, I'd still like to understand what the underlying problem is.

[rafapereirabr]

Hi all. There could be different things happening here.

• Possible cause: GTFS quality: Some cases might result from GTFS with poor quality an internal inconsistencies.

  • suggestion: if you want to investigate whether this is your case, I suggest using the Canonical GTFS Schedule Validator. You can use this tool directly on the link, or use it via the {gtfstools} pacakge in R. See this vignette. The package is currently out of CRAN and going through maintenance, but you can use the dev version from github

• Possible cause: extented route types: There is a posibility that R5 cannot deal with some particular extented route types

  • I don't think this is the case because, according to this, the Conveyal team has already accounted for R5 extented route types (e.g. route_type 1501) a long time ago.

• Possible cause: the latest version of R5 being more strict with GTFS quality

  • I don't know if this is the case.

A temporary fix, and which allows you to test if this possible cause is plausible, is to use the previous version of {r5r}. The code below install the previous version of r5r v1.1.0, which was built on top of R5 v6.9.0 Please note that this older version depended on Java 11.

# install java 11
rJavaEnv::java_quick_install(version = 11)

# install previous version of r5r that 
remotes::install_version("r5r", version = "1.1.0")

If all you could, please try running your analyses with the previous version of r5r and let us know if it works.

[erik-toi]

Thanks a lot for your tips. I tried the third alternative, installing the previous version of r5r, and it works. I was able to calculate transit trips with the same gtfs file.

[soikot733]

I am facing the same issue; sometimes I got ttm without any observation. I am working for Berlin city.

[soikot733]

Hi all. There could be different things happening here.

• Possible cause: GTFS quality: Some cases might result from GTFS with poor quality an internal inconsistencies.

  • suggestion: if you want to investigate whether this is your case, I suggest using the Canonical GTFS Schedule Validator. You can use this tool directly on the link, or use it via the {gtfstools} pacakge in R. See this vignette. The package is currently out of CRAN and going through maintenance, but you can use the dev version from github

• Possible cause: extented route types: There is a posibility that R5 cannot deal with some particular extented route types

  • I don't think this is the case because, according to this, the Conveyal team has already accounted for R5 extented route types (e.g. route_type 1501) a long time ago.

• Possible cause: the latest version of R5 being more strict with GTFS quality

  • I don't know if this is the case.

A temporary fix, and which allows you to test if this possible cause is plausible, is to use the previous version of {r5r}. The code below install the previous version of r5r v1.1.0, which was built on top of R5 v6.9.0 Please note that this older version depended on Java 11.

# install java 11
rJavaEnv::java_quick_install(version = 11)

# install previous version of r5r that 
remotes::install_version("r5r", version = "1.1.0")

If all you could, please try running your analyses with the previous version of r5r and let us know if it works.

Installing package into ‘C:/Users/shaka/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
Error: could not find function "install.packages"
Execution halted
Warning message:
In i.p(...) :
installation of package ‘C:/Users/shaka/AppData/Local/Temp/RtmpuQDqTO/file1f04141f49d0/r5r_2.0.0.9000.tar.gz’ had non-zero exit status

[soikot733]

Hi all. There could be different things happening here.

• Possible cause: GTFS quality: Some cases might result from GTFS with poor quality an internal inconsistencies.

  • suggestion: if you want to investigate whether this is your case, I suggest using the Canonical GTFS Schedule Validator. You can use this tool directly on the link, or use it via the {gtfstools} pacakge in R. See this vignette. The package is currently out of CRAN and going through maintenance, but you can use the dev version from github

• Possible cause: extented route types: There is a posibility that R5 cannot deal with some particular extented route types

  • I don't think this is the case because, according to this, the Conveyal team has already accounted for R5 extented route types (e.g. route_type 1501) a long time ago.

• Possible cause: the latest version of R5 being more strict with GTFS quality

  • I don't know if this is the case.

A temporary fix, and which allows you to test if this possible cause is plausible, is to use the previous version of {r5r}. The code below install the previous version of r5r v1.1.0, which was built on top of R5 v6.9.0 Please note that this older version depended on Java 11.

# install java 11
rJavaEnv::java_quick_install(version = 11)

# install previous version of r5r that 
remotes::install_version("r5r", version = "1.1.0")

If all you could, please try running your analyses with the previous version of r5r and let us know if it works.

Error: could not find function "install.packages"
Execution halted
Warning messages:
1: In i.p(...) : installation of package ‘sys’ had non-zero exit status
2: In i.p(...) : installation of package ‘units’ had non-zero exit status
3: In i.p(...) : installation of package ‘mime’ had non-zero exit status
4: In i.p(...) :
installation of package ‘askpass’ had non-zero exit status
5: In i.p(...) :
installation of package ‘openssl’ had non-zero exit status
6: In i.p(...) : installation of package ‘httr’ had non-zero exit status
7: In i.p(...) :
installation of package ‘C:/Users/shaka/AppData/Local/Temp/RtmpMZ4quA/remotes13207b2b4c53/r5r’ had non-zero exit status
I got this when trying to install r5r old version. any solution??

[e-kotov]

Error: could not find function "install.packages"

That looks very weird. Can you try this solution? https://forum.posit.co/t/error-could-not-find-function-install-packages-for-r-markdown/139782/2

[soikot733]

this the errors I received sometimes travel time matrix created with 0 observation. Is there anyone who can help me???

[rafapereirabr]

@soikot733 , could you please provide a sample of your data and the code you're using?

[soikot733]

Destination: ber_air.csv
Origin: Berlin_censos.csv
GTFS: https://www.opendata-oepnv.de/ht/de/organisation/verkehrsverbuende/vbb/startseite?tx_vrrkit_view%5Baction%5D=details&tx_vrrkit_view%5Bcontroller%5D=View&tx_vrrkit_view%5Bdataset_name%5D=soll-fahrplandaten-vbb&cHash=1a3b902c229b8ff5d26f2220434c3a5c
OSM: https://download.geofabrik.de/europe/germany/brandenburg.html

allocate RAM memory to Java before loading the {r5r} library

options(java.parameters = "-Xmx8G")

install.packages("r5r")
library(r5r)

path <- "D:/TUM/Civil Engineering/Traffic Control and Transport/Thesis/Data/Berlin"
r5r_core <- setup_r5(data_path = path, overwrite = TRUE)

Load origin/destination points and set arguments

o_points <- read.csv("D:/TUM/Civil Engineering/Traffic Control and Transport/Thesis/Data/Berlin/Berlin_censos.csv")
d_points <- read.csv("D:/TUM/Civil Engineering/Traffic Control and Transport/Thesis/Data/Berlin/ber_air.csv")
mode <- c("TRANSIT")
max_walk_time <- 10 # minutes
walk_speed <- 5 # kph
max_trip_duration <- 90 # minutes

departure datetime

departure_datetime <- as.POSIXct("10-03-2025 09:00:00",
format = "%d-%m-%Y %H:%M:%S")

3.1) calculate a travel time matrix

ttm <- travel_time_matrix(
r5r_core = r5r_core,
origins = o_points,
destinations = d_points,
mode = mode,
walk_speed = walk_speed,
departure_datetime = departure_datetime,
max_walk_time = max_walk_time,
max_trip_duration = max_trip_duration
)

Write the travel time matrix to a CSV file

location <- "D:/TUM/Civil Engineering/Traffic Control and Transport/Thesis/Data/Berlin/ttm.csv"
write.csv(ttm, location)

[kardemummabulle]

I could not make it work for Sweden with GTFS files I had. Had a question posted here for a while ago... Then eventually switched to OpenTripPlanner package and it worked nicely with the same data. Not sure why r5r failed, produced nice results for walking and biking, but refused to work with GTFS files. I tried everything that was mentioned in this repo - nothing helped...

[rafapereirabr]

Hi @kardemummabulle . We have a new version of the package on CRAN v2.1.0. Have you tried with the new version?

[soikot733]

Did you find any Solution for my error?? I tried also for whole day with different way but Output is Zero😔 Rafael H M Pereira ***@***.***> schrieb am Di. 11. März 2025 um 23:49:

…

Hi @kardemummabulle <https://github.com/kardemummabulle> . We have a new version of the package on CRAN v2.1.0. Have you tried with the new version? — Reply to this email directly, view it on GitHub <#398 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BPWWDSKMYW5TXYE32WTHVRD2T5SADAVCNFSM6AAAAABMQK2SC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMJVHA3TGNZRGA> . You are receiving this because you were mentioned.Message ID: ***@***.***> [image: rafapereirabr]*rafapereirabr* left a comment (ipeaGIT/r5r#398) <#398 (comment)> Hi @kardemummabulle <https://github.com/kardemummabulle> . We have a new version of the package on CRAN v2.1.0. Have you tried with the new version? — Reply to this email directly, view it on GitHub <#398 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BPWWDSKMYW5TXYE32WTHVRD2T5SADAVCNFSM6AAAAABMQK2SC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMJVHA3TGNZRGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[rafapereirabr]

Hi @soikot733 . As far as I could explore your data, it looks like your GTFS is fine. While exploring the GTFS of Berlin you shared, though, I've found a strange bug related to how {r5r} missread the spatial coordinates of transit trips#424. We'll be doing some investigation on this.

[kardemummabulle]

Hi @rafapereirabr ,

Have not tried with the new version yet, but gonna do that and report back :)