write_project function kills R

[ricschuster]

Hi Jeff,

I've just modified your Ontario pilot data script and got all the way to the write_project part:

## save project to disk
write_project(
  x = append(themes, append(includes, weights)),
  dataset = dataset,
  name = "Quebec pilot dataset",
  path =
    "out/quebec_pilot/quebec_pilot.yaml",
  spatial_path =
    "out/quebec_pilot/quebec_pilot_spatial.tif",
  attribute_path =
    "out/quebec_pilot/quebec_pilot_attribute.csv.gz",
  boundary_path =
    "out/quebec_pilot/quebec_pilot_boundary.csv.gz",
  mode = "advanced"
)

When I go ahead and run this code my R session quits. No warning or anything, it just closes. Do you have ideas how to trouble shoot this?

[jeffreyhanson]

Hmm, that's weird. Can you send me the script and I'll take a look at it?

[ricschuster]

Data and script are here: https://github.com/ricschuster/Tool1_pilot_QC
prep_Tool1_update.R
Thanks Jeff!

[jeffreyhanson]

When you run the code, do any of the files get created in the output folder or only some of them?

[jeffreyhanson]

I noticed that some of the theme/feature/include/weights names had accents - I wonder if this could be causing issues?

[ricschuster]

When you run the code, do any of the files get created in the output folder or only some of them?

None of them.

[ricschuster]

I noticed that some of the theme/feature/include/weights names had accents - I wonder if this could be causing issues?

That could be it. Will try changing them tomorrow.

[jeffreyhanson]

Ok - this suggests that it might be code writing the YAML file that is failing (since this is the first file that should be written).

What happens if you try running the following code (after running everything except write_project(...) in the script)?

# rename variables based on write_project parameters
x = append(themes, append(includes, weights)),
dataset = dataset,
name = "Quebec pilot dataset",
path =
  "out/quebec_pilot/quebec_pilot.yaml",
spatial_path =
  "out/quebec_pilot/quebec_pilot_spatial.tif",
attribute_path =
  "out/quebec_pilot/quebec_pilot_attribute.csv.gz",
boundary_path =
  "out/quebec_pilot/quebec_pilot_boundary.csv.gz",
mode = "advanced"

# code copied from write_project
## create setting list for themes
themes_idx <- vapply(x, inherits, what = "Theme", logical(1))
themes_params <- lapply(x[themes_idx], function(x) x$export())

## create setting list for weights
weights_idx <- vapply(x, inherits, what = "Weight", logical(1))
weights_params <- lapply(x[weights_idx], function(x) x$export())

## create setting list for includes
includes_idx <- vapply(x, inherits, what = "Include", logical(1))
includes_params <- lapply(x[includes_idx], function(x) x$export())

## create full settings list
params <- list(
  name = name,
  spatial_path = basename(spatial_path),
  attribute_path = basename(attribute_path),
  boundary_path = basename(boundary_path),
  mode = mode,
  themes = themes_params,
  weights = weights_params,
  includes = includes_params
)

## save configuration file to disk
yaml::write_yaml(params, path)

[ricschuster]

R still crashes without throwing an error.
I've also tried the accents and unless I've missed some, the problem persists.

[ricschuster]

It was the . in some of the variable names that messed things up. I've replaced them with and it works now.

[ricschuster]

I did push the project to the server, but now get this error:

Do you have a way to test projects setup, so I can figure out what went wrong?

[jeffreyhanson]

Yeah, if you clone the repo, and then use make debug, then it will launch the app locally. Now it will print stuff to the console when you get an error. You can import the project manually to test it (i.e. manually uploding project files). Does that help?

[jeffreyhanson]

Or, just copy in the project files into ./inst/extdata/projects temporarily to debug it (but don't push these files to GitHub unless you want them included as a built-in demo dataset).

[jeffreyhanson]

It was the . in some of the variable names that messed things up. I've replaced them with and it works now.

To avoid this in the future, I'll update the code so that you can't create variable with a . its name (i.e. it will throw an error).

[ricschuster]

Thanks!

[jeffreyhanson]

Ah - just to be clear do you mean the "index" for a varible? I just checked and variables don't have "name" (strictly speaking).

[jeffreyhanson]

It's the theme/include/weight name specifically.

[ricschuster]

I've finally got the pilot data to work on the server.
The yaml issue, we've already addressed/talked about.

The rest was related to the special characters in French. I had to convert them all to 'normal' characters for this to work. I did it for both the layer names and the variable names. Not sure why this is an issue.

[jeffreyhanson]

It seems that the encoding issue is related to the yaml R package (see vubiostat/r-yaml#90). To address this, I'll try wrapping the names in enc2utf8(...) before writing them to disk.