Add a "quiet" argument to setup_r5 about r5r

[rafapereirabr]

I agree this would be a good addition to the function and we should add this paremeter to the routing functions as well. I've done a quick search on how to supress messages from Java but couldn't find a way. @mvpsaraiva is the Java expert among us, so hopefully he'll know how to address this

[mvpsaraiva]

I'll try to figure this out. I thought it would be easier to suppress logging messages from the R side, but I'll check how to do it directly in Java.

[dhersz]

It shouldn't be that hard with sink(). I'm having a look at it now.

[dhersz]

Well, it really shouldn't be hard, but it's not working, not sure why. With sink we can collect either outputs (print, cat, etc) or messages (messages, warnings, errors), but none of these seem to work with setup_r5.

Some reproducible code:

data_path <- system.file("extdata", package = "r5r")
logs_path <- file.path(data_path, "setup_logs.txt")
logs      <- file(logs_path, open = "w")

sink(logs, type = "message")

setup_r5(system.file("extdata", package = "r5r"))

sink(NULL, type = "message")
close(logs)

Creates a log with the following content:

Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0.jar

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

When setting type = "output":

data_path <- system.file("extdata", package = "r5r")
logs_path <- file.path(data_path, "setup_logs.txt")
logs      <- file(logs_path, open = "w")

sink(logs, type = "output")

setup_r5(system.file("extdata", package = "r5r"))

sink(NULL, type = "output")
close(logs)

The log:
[1] "Java-Object{com.conveyal.r5.R5RCore@2dc4be3a}"

None prevent the log messages from appearing in the console, however...

[mvpsaraiva]

I've added a quiet argument to the setup_r5 function. It wasn't a trivial task, and it definitely needs more testing, but I think it is working.

I've also created a set of functions to control how verbose R5R core is. Some examples:

# Most messages are shown. It is the default now.
r5r_core$verboseMode()

# Only errors are reported.
r5r_core$silentMode()

# Additional function to fine tune the outputs:
# everything
r5r_core$setLogMode("ALL")

# completely silent
r5r_core$setLogMode("OFF")

# somewhere in between
r5r_core$setLogMode("ERROR")
r5r_core$setLogMode("WARN")
r5r_core$setLogMode("INFO")
r5r_core$setLogMode("DEBUG")
r5r_core$setLogMode("TRACE")

The new logging mode takes effect after one of those functions is called. Now we need to create the R wrapper functions around those.

[rafapereirabr]

I've created a new support function set_verbose() (see below). I've implemented it in the travel_time_matrix function as a first test and it seems to be working fine. The default behavior is verbose=TRUE to show R5 output messages r5r_core$verboseMode() but the user can set verbose=FALSE to get only ERROR messages, if there are any.

Let me know if you guys are Ok with this, and then we can proceed to implemented in the other functions.

#' Set verbose argument
#'
#' @param verbose logical, passed from function above
#' @export
#' @family support functions
#'
set_verbose <- function(verbose){

  if (verbose == TRUE) {
    r5r_core$verboseMode()

  } else if (verbose == FALSE) {
    # Only errors are reported.
    r5r_core$silentMode()

  } else {
    stop("Parameter 'verbose' must be either TRUE or FALSE")
  }
}

[rafapereirabr]

@mvpsaraiva , I've noticed you included a quiet parameter to setup_r5. We are using a verbose parameter in the routing functions with th same purpose (see below). I suggest we use the same parameter name and description in the documentation.
I suggest we use verbose becasue the download_r5 already has a quiet argument. Let me know what you think

#' @param quiet boolean value indicating if R5 should be started in 'quiet mode',
#'              when only error messages are output to the console.

vs

#' @param verbose logical, TRUE to show detailed output messages (Default) or
#'                FALSE to show only eventual ERROR messages.

[mvpsaraiva]

I agree that verbose would be better, to keep it standard. I will change this in Java as well, so we don't have to pass a quiet = !verbose parameter to the rJava call.

[mvpsaraiva]

dab7cf9

[dhersz]

setup_r5 logs the same messages in console for me when verbose is set to either TRUE or FALSE (see below). Is this the desired behaviour? If I recall correctly more messages used to be logged.

> r5r_obj <- setup_r5(data_path, verbose = FALSE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200819.jar
Summarizing builder config: build-config.json
{
  "htmlAnnotations" : false,
  "maxHtmlAnnotationsPerFile" : 1000,
  "transit" : true,
  "useTransfersTxt" : false,
  "parentStopLinking" : false,
  "stationTransfers" : false,
  "subwayAccessTime" : 2.0,
  "streets" : true,
  "embedRouterConfig" : true,
  "areaVisibility" : false,
  "matchBusRoutesToStreets" : false,
  "fetchElevationUS" : false,
  "speeds" : {
    "units" : "mph",
    "values" : {
      "secondary" : 35,
      "tertiary_link" : 25,
      "primary_link" : 25,
      "tertiary" : 25,
      "living_street" : 5,
      "motorway_link" : 35,
      "trunk" : 55,
      "secondary_link" : 25,
      "motorway" : 65,
      "trunk_link" : 35,
      "primary" : 45
    },
    "defaultSpeed" : 25
  },
  "staticBikeRental" : false,
  "staticParkAndRide" : true,
  "staticBikeParkAndRide" : false,
  "bikeRentalFile" : null,
  "analysisFareCalculator" : null
}

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat
> stop_r5(r5r_obj)
r5r_obj has been successfully stopped.
> r5r_obj <- setup_r5(data_path, verbose = TRUE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200819.jar
Summarizing builder config: build-config.json
{
  "htmlAnnotations" : false,
  "maxHtmlAnnotationsPerFile" : 1000,
  "transit" : true,
  "useTransfersTxt" : false,
  "parentStopLinking" : false,
  "stationTransfers" : false,
  "subwayAccessTime" : 2.0,
  "streets" : true,
  "embedRouterConfig" : true,
  "areaVisibility" : false,
  "matchBusRoutesToStreets" : false,
  "fetchElevationUS" : false,
  "speeds" : {
    "units" : "mph",
    "values" : {
      "secondary" : 35,
      "tertiary_link" : 25,
      "primary_link" : 25,
      "tertiary" : 25,
      "living_street" : 5,
      "motorway_link" : 35,
      "trunk" : 55,
      "secondary_link" : 25,
      "motorway" : 65,
      "trunk_link" : 35,
      "primary" : 45
    },
    "defaultSpeed" : 25
  },
  "staticBikeRental" : false,
  "staticParkAndRide" : true,
  "staticBikeParkAndRide" : false,
  "bikeRentalFile" : null,
  "analysisFareCalculator" : null
}

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

[dhersz]

Some more tests:

> r5r_obj <- setup_r5(data_path, verbose = TRUE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200819.jar
Summarizing builder config: build-config.json
{
  "htmlAnnotations" : false,
  "maxHtmlAnnotationsPerFile" : 1000,
  "transit" : true,
  "useTransfersTxt" : false,
  "parentStopLinking" : false,
  "stationTransfers" : false,
  "subwayAccessTime" : 2.0,
  "streets" : true,
  "embedRouterConfig" : true,
  "areaVisibility" : false,
  "matchBusRoutesToStreets" : false,
  "fetchElevationUS" : false,
  "speeds" : {
    "units" : "mph",
    "values" : {
      "secondary" : 35,
      "tertiary_link" : 25,
      "primary_link" : 25,
      "tertiary" : 25,
      "living_street" : 5,
      "motorway_link" : 35,
      "trunk" : 55,
      "secondary_link" : 25,
      "motorway" : 65,
      "trunk_link" : 35,
      "primary" : 45
    },
    "defaultSpeed" : 25
  },
  "staticBikeRental" : false,
  "staticParkAndRide" : true,
  "staticBikeParkAndRide" : false,
  "bikeRentalFile" : null,
  "analysisFareCalculator" : null
}

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

> r5r_obj <- setup_r5(data_path, verbose = FALSE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200819.jar
Summarizing builder config: build-config.json
{
  "htmlAnnotations" : false,
  "maxHtmlAnnotationsPerFile" : 1000,
  "transit" : true,
  "useTransfersTxt" : false,
  "parentStopLinking" : false,
  "stationTransfers" : false,
  "subwayAccessTime" : 2.0,
  "streets" : true,
  "embedRouterConfig" : true,
  "areaVisibility" : false,
  "matchBusRoutesToStreets" : false,
  "fetchElevationUS" : false,
  "speeds" : {
    "units" : "mph",
    "values" : {
      "secondary" : 35,
      "tertiary_link" : 25,
      "primary_link" : 25,
      "tertiary" : 25,
      "living_street" : 5,
      "motorway_link" : 35,
      "trunk" : 55,
      "secondary_link" : 25,
      "motorway" : 65,
      "trunk_link" : 35,
      "primary" : 45
    },
    "defaultSpeed" : 25
  },
  "staticBikeRental" : false,
  "staticParkAndRide" : true,
  "staticBikeParkAndRide" : false,
  "bikeRentalFile" : null,
  "analysisFareCalculator" : null
}

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

> stop_r5(r5r_obj)
r5r_obj has been successfully stopped.

> r5r_obj <- setup_r5(data_path, verbose = FALSE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200819.jar
11:33:40.177 [main] INFO  c.c.r5.transit.TransportNetwork - File 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\build-config.json' is not present. Using default configuration.
11:33:40.178 [main] INFO  c.c.r5.transit.TransportNetwork - Found GTFS file C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa.zip
11:33:40.178 [main] WARN  c.c.r5.transit.TransportNetwork - Skipping non-input file 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_hexgrid.csv'
11:33:40.178 [main] INFO  c.c.r5.transit.TransportNetwork - Found OSM file C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_osm.pbf
11:33:40.178 [main] WARN  c.c.r5.transit.TransportNetwork - Skipping non-input file 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_osm.pbf.mapdb'
11:33:40.178 [main] WARN  c.c.r5.transit.TransportNetwork - Skipping non-input file 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_osm.pbf.mapdb.p'
11:33:40.178 [main] WARN  c.c.r5.transit.TransportNetwork - Skipping non-input file 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_points_of_interest.csv'
Summarizing builder config: build-config.json
{
  "htmlAnnotations" : false,
  "maxHtmlAnnotationsPerFile" : 1000,
  "transit" : true,
  "useTransfersTxt" : false,
  "parentStopLinking" : false,
  "stationTransfers" : false,
  "subwayAccessTime" : 2.0,
  "streets" : true,
  "embedRouterConfig" : true,
  "areaVisibility" : false,
  "matchBusRoutesToStreets" : false,
  "fetchElevationUS" : false,
  "speeds" : {
    "units" : "mph",
    "values" : {
      "secondary" : 35,
      "tertiary_link" : 25,
      "primary_link" : 25,
      "tertiary" : 25,
      "living_street" : 5,
      "motorway_link" : 35,
      "trunk" : 55,
      "secondary_link" : 25,
      "motorway" : 65,
      "trunk_link" : 35,
      "primary" : 45
    },
    "defaultSpeed" : 25
  },
  "staticBikeRental" : false,
  "staticParkAndRide" : true,
  "staticBikeParkAndRide" : false,
  "bikeRentalFile" : null,
  "analysisFareCalculator" : null
}
11:33:40.183 [main] INFO  com.conveyal.osmlib.OSM - Reading OSM DB from: C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa_osm.pbf.mapdb
11:33:40.192 [main] INFO  com.conveyal.osmlib.OSM - Not reading from file since database is already filled!
11:33:40.192 [main] INFO  com.conveyal.osmlib.OSM - Detecting intersections...
11:33:40.285 [main] INFO  com.conveyal.osmlib.OSM - Done detecting intersections.
11:33:40.288 [main] INFO  com.conveyal.r5.streets.StreetLayer - Making street edges from OSM ways...
11:33:40.666 [main] INFO  com.conveyal.r5.streets.StreetLayer - Surrogate LTS:
  1: 32730 edges
  2: 7079 edges
  3: 723 edges
  4: 9244 edges
  Unknown: 7134 edges
11:33:40.668 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done making street edges.
11:33:40.668 [main] INFO  com.conveyal.r5.streets.StreetLayer - Made 20826 vertices and 56910 edges.
11:33:40.668 [main] INFO  com.conveyal.r5.streets.StreetLayer - Found 0 P+R node candidates
11:33:40.668 [main] INFO  com.conveyal.r5.streets.StreetLayer - Building edge lists from edges...
11:33:40.670 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done building edge lists.
11:33:40.675 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removing islands for mode CAR
11:33:40.690 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Found 5733 strong components for mode CAR using Tarjan's algorithm in 0.015sec
11:33:40.691 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removed 5731 strong component (islands) with fewer than 40 vertices for mode CAR in 0.001sec. 5942 vertices removed.
11:33:40.691 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removing islands for mode WALK
11:33:40.709 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Found 1959 strong components for mode WALK using Tarjan's algorithm in 0.018sec
11:33:40.710 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removed 1957 strong component (islands) with fewer than 40 vertices for mode WALK in 0.001sec. 2403 vertices removed.
11:33:40.710 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removing islands for mode BICYCLE
11:33:40.728 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Found 2154 strong components for mode BICYCLE using Tarjan's algorithm in 0.018sec
11:33:40.730 [main] INFO  c.c.r5.streets.TarjanIslandPruner - Removed 2152 strong component (islands) with fewer than 40 vertices for mode BICYCLE in 0.001sec. 2285 vertices removed.
11:33:40.730 [main] INFO  com.conveyal.r5.streets.StreetLayer - Indexing streets...
11:33:40.772 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done indexing streets.
11:33:40.773 [main] INFO  com.conveyal.r5.streets.StreetLayer - Made 0 P+R vertices
11:33:40.773 [main] INFO  com.conveyal.r5.streets.StreetLayer - Created 0 turn restrictions
11:33:40.820 [main] INFO  com.conveyal.r5.streets.StreetLayer - Indexing streets...
11:33:40.852 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done indexing streets.
11:33:41.055 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table feed_info was missing but it is not required.
11:33:41.055 [main] INFO  com.conveyal.gtfs.GTFSFeed - Feed ID is undefined, pester maintainers to include a feed ID. Using file name poa.
11:33:41.055 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table agency from agency.txt
11:33:41.056 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table calendar from calendar.txt
11:33:41.057 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table calendar_dates was missing but it is not required.
11:33:41.059 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table fare_attributes was missing but it is not required.
11:33:41.059 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table fare_rules was missing but it is not required.
11:33:41.059 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table routes from routes.txt
11:33:41.059 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table shapes from shapes.txt
11:33:41.062 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table stops from stops.txt
11:33:41.063 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table transfers was missing but it is not required.
11:33:41.063 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table trips from trips.txt
11:33:41.065 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Table frequencies was missing but it is not required.
11:33:41.065 [main] INFO  c.conveyal.gtfs.model.Entity$Loader - Loading GTFS table stop_times from stop_times.txt
11:33:41.197 [main] INFO  com.conveyal.gtfs.GTFSFeed - 0 errors
11:33:41.211 [main] INFO  com.conveyal.gtfs.GTFSFeed - Generating unique names for patterns
11:33:41.212 [main] INFO  com.conveyal.gtfs.GTFSFeed - Total patterns: 4
11:33:41.212 [main] INFO  com.conveyal.r5.transit.TransitLayer - Creating trip patterns and schedules.
11:33:41.219 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 5776 on trip 176-1@1#2310 on route 176, skipping this trip as it will wreak havoc with routing
11:33:41.250 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 454 on trip A141-1@3#2340 on route A141, skipping this trip as it will wreak havoc with routing
11:33:41.250 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 454 on trip A141-1@5#2340 on route A141, skipping this trip as it will wreak havoc with routing
11:33:41.303 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@1#2310 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.304 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@1#2332 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.305 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@1#2357 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.334 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@2#2332 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.334 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@2#2357 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.346 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@5#2334 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.346 [main] WARN  com.conveyal.r5.transit.TransitLayer - Negative-time travel at stop 3608 on trip T2-1@5#2357 on route T2, skipping this trip as it will wreak havoc with routing
11:33:41.349 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done creating 377 trips on 4 patterns.
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - 0 zero-duration hops found.
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - Chaining trips together according to blocks to model interlining...
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done chaining trips together according to blocks.
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - Sorting trips on each pattern
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - done sorting
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - Finding the approximate center of the transport network...
11:33:41.350 [main] INFO  com.conveyal.r5.transit.TransitLayer - TransportNetwork time zone set to America/Sao_Paulo from agency 'Empresa Publica de Transportes e Circula��o' and agency_timezone:America/Sao_Paulo
11:33:41.395 [main] INFO  com.conveyal.r5.streets.StreetLayer - Indexing streets...
11:33:41.415 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done indexing streets.
11:33:41.423 [main] INFO  com.conveyal.r5.streets.StreetLayer - Building edge lists from edges...
11:33:41.426 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done building edge lists.
11:33:41.426 [main] INFO  com.conveyal.r5.transit.TransitLayer - Rebuilding transient indices.
11:33:41.426 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done rebuilding transient indices.
11:33:41.426 [main] INFO  c.conveyal.r5.transit.TransferFinder - Finding transfers through the street network from 212 stops...
11:33:41.473 [main] INFO  c.conveyal.r5.transit.TransferFinder - Done finding transfers. 86 stops were not linked to the street network.
11:33:41.473 [main] INFO  c.conveyal.r5.transit.TransferFinder - Finding closest stops to P+R for 0 P+Rs
11:33:41.473 [main] INFO  c.conveyal.r5.transit.TransferFinder - Found 0 unconnected P+Rs and 0 P+Rs without closest stop in 500 m
11:33:41.474 [main] INFO  c.c.r5.kryo.KryoNetworkSerializer - Writing transport network...
11:33:41.521 [main] INFO  c.c.r5.kryo.KryoNetworkSerializer - Done writing.
11:33:41.521 [main] INFO  c.c.r5.kryo.KryoNetworkSerializer - Reading transport network...
11:33:41.522 [main] INFO  c.c.r5.kryo.KryoNetworkSerializer - Loading R5NETWORK file saved by R5 version 4.9.0-SNAPSHOT commit 0719b6c6c5f39c5de1f33fd33a4c7d2857ebd87e
11:33:41.556 [main] INFO  c.c.r5.kryo.KryoNetworkSerializer - Done reading.
11:33:41.556 [main] INFO  com.conveyal.r5.streets.StreetLayer - Building edge lists from edges...
11:33:41.558 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done building edge lists.
11:33:41.558 [main] INFO  com.conveyal.r5.streets.StreetLayer - Indexing streets...
11:33:41.581 [main] INFO  com.conveyal.r5.streets.StreetLayer - Done indexing streets.
11:33:41.581 [main] INFO  com.conveyal.r5.transit.TransitLayer - Rebuilding transient indices.
11:33:41.581 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done rebuilding transient indices.
11:33:41.581 [main] INFO  com.conveyal.r5.transit.TransitLayer - Finding distances from transit stops to street vertices.
11:33:41.581 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 66 has not been linked to the street network, cannot build a distance table for it.
11:33:41.596 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 68 has not been linked to the street network, cannot build a distance table for it.
11:33:41.602 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 134 has not been linked to the street network, cannot build a distance table for it.
11:33:41.606 [ForkJoinPool.commonPool-worker-1] WARN  com.conveyal.r5.transit.TransitLayer - Stop 15 has not been linked to the street network, cannot build a distance table for it.
11:33:41.606 [ForkJoinPool.commonPool-worker-1] WARN  com.conveyal.r5.transit.TransitLayer - Stop 16 has not been linked to the street network, cannot build a distance table for it.
11:33:41.612 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 137 has not been linked to the street network, cannot build a distance table for it.
11:33:41.612 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 138 has not been linked to the street network, cannot build a distance table for it.
11:33:41.612 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 139 has not been linked to the street network, cannot build a distance table for it.
11:33:41.616 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 73 has not been linked to the street network, cannot build a distance table for it.
11:33:41.619 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 142 has not been linked to the street network, cannot build a distance table for it.
11:33:41.630 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 76 has not been linked to the street network, cannot build a distance table for it.
11:33:41.630 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 77 has not been linked to the street network, cannot build a distance table for it.
11:33:41.630 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 78 has not been linked to the street network, cannot build a distance table for it.
11:33:41.685 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 148 has not been linked to the street network, cannot build a distance table for it.
11:33:41.695 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 56 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 154 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 155 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 156 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 157 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 158 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 119 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 120 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 121 has not been linked to the street network, cannot build a distance table for it.
11:33:41.701 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 122 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 59 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 60 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 61 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 62 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 63 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 64 has not been linked to the street network, cannot build a distance table for it.
11:33:41.707 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 65 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 94 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 95 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 96 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 97 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 98 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 99 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 100 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 101 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 102 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 103 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 104 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 105 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 79 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 80 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 81 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 82 has not been linked to the street network, cannot build a distance table for it.
11:33:41.719 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 83 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 106 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 107 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 108 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 109 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 110 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 111 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 112 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 113 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 114 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 115 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 116 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 117 has not been linked to the street network, cannot build a distance table for it.
11:33:41.748 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 118 has not been linked to the street network, cannot build a distance table for it.
11:33:41.762 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 187 has not been linked to the street network, cannot build a distance table for it.
11:33:41.762 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 188 has not been linked to the street network, cannot build a distance table for it.
11:33:41.762 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 189 has not been linked to the street network, cannot build a distance table for it.
11:33:41.762 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 190 has not been linked to the street network, cannot build a distance table for it.
11:33:41.762 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 191 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 193 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 194 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 195 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 196 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 197 has not been linked to the street network, cannot build a distance table for it.
11:33:41.769 [main] WARN  com.conveyal.r5.transit.TransitLayer - Stop 198 has not been linked to the street network, cannot build a distance table for it.
11:33:41.770 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 174 has not been linked to the street network, cannot build a distance table for it.
11:33:41.774 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 176 has not been linked to the street network, cannot build a distance table for it.
11:33:41.801 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 183 has not been linked to the street network, cannot build a distance table for it.
11:33:41.809 [ForkJoinPool.commonPool-worker-1] WARN  com.conveyal.r5.transit.TransitLayer - Stop 0 has not been linked to the street network, cannot build a distance table for it.
11:33:41.809 [ForkJoinPool.commonPool-worker-1] WARN  com.conveyal.r5.transit.TransitLayer - Stop 1 has not been linked to the street network, cannot build a distance table for it.
11:33:41.824 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 159 has not been linked to the street network, cannot build a distance table for it.
11:33:41.825 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 160 has not been linked to the street network, cannot build a distance table for it.
11:33:41.834 [ForkJoinPool.commonPool-worker-5] WARN  com.conveyal.r5.transit.TransitLayer - Stop 50 has not been linked to the street network, cannot build a distance table for it.
11:33:41.850 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 164 has not been linked to the street network, cannot build a distance table for it.
11:33:41.850 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 165 has not been linked to the street network, cannot build a distance table for it.
11:33:41.855 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 167 has not been linked to the street network, cannot build a distance table for it.
11:33:41.855 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 168 has not been linked to the street network, cannot build a distance table for it.
11:33:41.855 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 169 has not been linked to the street network, cannot build a distance table for it.
11:33:41.855 [ForkJoinPool.commonPool-worker-7] WARN  com.conveyal.r5.transit.TransitLayer - Stop 170 has not been linked to the street network, cannot build a distance table for it.
11:33:41.884 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done. Computed distances to street vertices from 212 of 212 transit stops.

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

[rafapereirabr]

I don't think this is ideal, but I'm Ok with R5 printing this small ouput of Summarizing builder config: build-config.json

I just noticed, however, this outputs says speed is measured in "units" : "mph" . Now I'm confused with the setting speeds for waking and cycling

[mvpsaraiva]

I just noticed, however, this outputs says speed is measured in "units" : "mph" . Now I'm confused with the setting speeds for waking and cycling

Those are the default speeds it is using for each kind of road segment. Internally, they are all converted into metres per second, which is the unit we use.

[mvpsaraiva]

I think this function is not working properly for you because it depends on the new .jar file I'm working on now.

[dhersz]

While I'm okay with it printing the build-config.json, it's important to note that I set verbose = FALSE in the example in the second post and it didn't work.

But since Marcus suggested it might be a problem with the jar then I'll oficially play the waiting game hehe

[mvpsaraiva]

The build-config.json file now is printed only when verbose = TRUE.

[dhersz]

Something is still going on. After I set verbose = FALSE once all subsequent setups will be verbose, irrespective of what value I'm passing. Check it out (I supressed quite a bit of the log messages for readability):

> data_path <- system.file("extdata", package = "r5r")
> r5r_obj <- setup_r5(data_path, verbose = TRUE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200822.jar
10:26:58.209 [main] INFO  c.c.r5.transit.TransportNetwork - File 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\build-config.json' is not present. Using default configuration.
10:26:58.248 [main] INFO  c.c.r5.transit.TransportNetwork - Found GTFS file C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\poa.zip
.............
10:27:08.684 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done. Computed distances to street vertices from 212 of 212 transit stops.

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat


> r5r_obj <- setup_r5(data_path, verbose = TRUE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200822.jar
10:28:19.893 [main] INFO  c.c.r5.transit.TransportNetwork - File 'C:\Users\Usuario\Documents\repos\r5r\r-package\inst\extdata\build-config.json' is not present. Using default configuration.
...................
10:28:24.244 [main] INFO  com.conveyal.r5.transit.TransitLayer - Done. Computed distances to street vertices from 212 of 212 transit stops.

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat


> r5r_obj <- setup_r5(data_path, verbose = FALSE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200822.jar

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat


> r5r_obj <- setup_r5(data_path, verbose = TRUE)
Using cached version from C:/Users/Usuario/Documents/R/win-library/4.0/r5r/jar/r5r_v4.9.0_20200822.jar

Using cached network.dat from C:/Users/Usuario/Documents/repos/r5r/r-package/inst/extdata/network.dat

[mvpsaraiva]

It's a bug. I've found it, and I'll fix for the next jar.
Thanks @dhersz

[rafapereirabr]

@mvpsaraiva , Can we close this now ?

[dhersz]

Seems to be working alright for me now. I'm closing it now, but we can always open it later if we find something related to it.