Get-my-data-in execution halted

[anelda]

When running the following code and also when following instructions in the afrilearnr README file I get the error below:

learnr::run_tutorial("get-my-data-in", "afrilearnr")

processing file: get-my-data-in.Rmd
  |.....                                                                                                          |   5%
  ordinary text without R code

  |..........                                                                                                     |   9%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |...............                                                                                                |  14%
  ordinary text without R code

  |....................                                                                                           |  18%
label: packages (with options) 
List of 1
 $ echo: logi TRUE

  |.........................                                                                                      |  23%
  ordinary text without R code

  |..............................                                                                                 |  27%
label: csv-airports (with options) 
List of 2
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE

Quitting from lines 88-104 (get-my-data-in.Rmd) 
Error: '' does not exist in current working directory ('/home/talarify/R/x86_64-pc-linux-gnu-library/4.0/afrilearnr/tutorials/get-my-data-in').

There is no way to recover and try an alternative tutorial if I click on Tutorial -> run tutorial in the tutorial tab. A "Loading tutorial" message appears with a circle that turns continuously and no back/stop button.

I restarted my R session, but the Loading tutorial message stays and wheel keeps on turning.

It works if I right click on the Tutorial tab and click on Reload

[andysouth]

My first guess is that it may be due to lines 90 & 91, and possible linux/windows differences.

filename <- system.file("extdata/afriairports.csv", package="afrilearndata")
mydf <- readr::read_csv(filename)

@anelda can you paste those two lines into your R console and see if they work ?

[anelda]

Hi @andysouth

Yes, the first line works, but the second line gives this error -

Error: '' does not exist in current working directory ('/home/talarify').

[andysouth]

Thanks @anelda @AnneMTreasure, this one should be fixed by 083e2e0
Can you reinstall & try again ? Thanks.

[AnneMTreasure]

Hi @andysouth,

I reinstalled, but when running the following code (on a mac):

learnr::run_tutorial("get-my-data-in", "afrilearnr")

I get this error:

processing file: get-my-data-in.Rmd
  |...                                                                   |   5%
  ordinary text without R code

  |......                                                                |   9%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |..........                                                            |  14%
  ordinary text without R code

  |.............                                                         |  18%
label: packages (with options) 
List of 1
 $ echo: logi TRUE

  |................                                                      |  23%
  ordinary text without R code

  |...................                                                   |  27%
label: csv-airports (with options) 
List of 2
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE


── Column specification ────────────────────────────────────────────────────────
cols(
  .default = col_character(),
  id = col_double(),
  latitude_deg = col_double(),
  longitude_deg = col_double(),
  elevation_ft = col_double(),
  scheduled_service = col_double(),
  score = col_double(),
  last_updated = col_datetime(format = "")
)
ℹ Use `spec()` for the full column specifications.

  |......................                                                |  32%
  ordinary text without R code

  |.........................                                             |  36%
label: csv-crs-missing (with options) 
List of 4
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE
 $ message      : logi FALSE
 $ warning      : logi FALSE


── Column specification ────────────────────────────────────────────────────────
cols(
  .default = col_character(),
  id = col_double(),
  latitude_deg = col_double(),
  longitude_deg = col_double(),
  elevation_ft = col_double(),
  scheduled_service = col_double(),
  score = col_double(),
  last_updated = col_datetime(format = "")
)
ℹ Use `spec()` for the full column specifications.

  |.............................                                         |  41%
  ordinary text without R code

  |................................                                      |  45%
label: dataframe-airports (with options) 
List of 1
 $ echo: logi TRUE

  |...................................                                   |  50%
  ordinary text without R code

  |......................................                                |  55%
label: dataframe-sf (with options) 
List of 4
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE
 $ message      : logi FALSE
 $ warning      : logi FALSE

  |.........................................                             |  59%
  ordinary text without R code

  |.............................................                         |  64%
label: shp-countries (with options) 
List of 4
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE
 $ message      : logi FALSE
 $ warning      : logi FALSE

  |................................................                      |  68%
  ordinary text without R code

  |...................................................                   |  73%
label: kml-highways (with options) 
List of 4
 $ exercise     : logi TRUE
 $ exercise.eval: logi TRUE
 $ message      : logi FALSE
 $ warning      : logi FALSE

Quitting from lines 228-236 (get-my-data-in.Rmd) 
Error in CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  : 
  Feature creation failed.
In addition: Warning messages:
1: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 1: ICreateFeature: Mismatched geometry type
2: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 6: DeleteLayer() not supported by this dataset.

I also get the same error as Anelda in the comment above when clicking on the tutorials using the tutorial tab (i.e. A "Loading tutorial" message appears with a circle that turns continuously and no back/stop button).

[AnneMTreasure]

Checking some of the other tutorials, when running:

learnr::run_tutorial("afrilearnr-crash-course", "afrilearnr")

I get the following message (also mentioned in issue #9):

Error: Tutorial "afrilearnr-crash-course" was not found in the "afrilearnr" package.
Available tutorials:
* afrilearnr
  - get-my-data-in     : "How to get your own spatial data into R"
  - openstreetmap-data : "Download and plot OpenStreetMap data from R"
  - template-tutorial  : "Blank afrimapr tutorial template"
  - test-tmap-view     : "test tmap failing in view mode when run by learner"

Of the tutorials currently shown as available in afrilearnr, get-my-data-in is the only one that doesn't load. The other three (openstreetmap-data, template-tutorial, test-tmap-view) all open and load in browser windows.

[andysouth]

Thanks @AnneMTreasure

So the problem which is causing it to fail on Mac & Linux, while it seems to be OK on Windows is shown by this :

Quitting from lines 228-236 (get-my-data-in.Rmd) 
Error in CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  : Feature creation failed.

CPL_write_OGR is (I think) a GDAL (Geospatial Data Abstraction Library) function. GDAL can operate differently on different systems.

Lines 228-236 contain this code which just reads in a kml and plots it :

filename <- system.file("extdata","trans-african-highway.kml", package="afrilearndata", mustWork=TRUE)
afrihighway <- sf::read_sf(filename)
mapview(afrihighway)

So this shouldn't be a problem, that code is not even writing anything, but is, and is tricky to fix.

Can you try the 3 lines of code above in your R console ?

[AnneMTreasure]

Hi @andysouth ,

Running this code:

filename <- system.file("extdata","trans-african-highway.kml", package="afrilearndata", mustWork=TRUE)
afrihighway <- sf::read_sf(filename)
mapview(afrihighway)

The first two lines run, but this one:

mapview(afrihighway)

gives this error:

Failed to create feature 0 in file2ba66c91965e
Deleting layer not supported by driver `FlatGeobuf'
Error in CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  : 
  Feature creation failed.
In addition: Warning messages:
1: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 1: ICreateFeature: Mismatched geometry type
2: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 6: DeleteLayer() not supported by this dataset.

[andysouth]

Thanks @AnneMTreasure seems to be a problem with either reading in or plotting the highways.

Can you try :
str(afrihighway)
head(afrihighway)

[AnneMTreasure]

Hi @andysouth, these work:

str(afrihighway)

sf[,3] [100 × 3] (S3: sf/tbl_df/tbl/data.frame)
 $ Name       : chr [1:100] "Western Sahara (Morocco) Link" "Mauritania Border- Dakar Link" "Nouakchott- Senegal Border Link" "Western Sahara Border- Nouakchott Link" ...
 $ Description: chr [1:100] "Cairo-Dakar Highway section linking Senegal across Western Sahara to Morocco. This highway is part of the great"| __truncated__ "" "" "" ...
 $ geometry   :sfc_LINESTRING of length 100; first list element:  'XYZ' num [1:18, 1:3] -16.9 -16.9 -16.5 -16.3 -16.1 ...
 - attr(*, "sf_column")= chr "geometry"
 - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
  ..- attr(*, "names")= chr [1:2] "Name" "Description"

head(afrihighway)

Simple feature collection with 6 features and 2 fields
Geometry type: LINESTRING
Dimension:     XYZ
Bounding box:  xmin: -17.36938 ymin: 14.76957 xmax: -6.800537 ymax: 33.98436
z_range:       zmin: 0 zmax: 0
Geodetic CRS:  WGS 84
# A tibble: 6 x 3
  Name          Description                                             geometry
  <chr>         <chr>                                           <LINESTRING [°]>
1 Western Saha… "Cairo-Dakar Highway secti… Z (-16.94778 21.34438 0, -16.85303 …
2 Mauritania B… ""                          Z (-17.36938 14.76957 0, -16.9519 1…
3 Nouakchott- … ""                          Z (-15.81069 16.52036 0, -16.11694 …
4 Western Saha… ""                          Z (-15.99128 18.08646 0, -16.01807 …
5 Marrakesh- W… ""                          Z (-12.95837 27.67623 0, -12.7002 2…
6 Rabat- Marra… ""                          Z (-8.12439 31.79238 0, -8.02002 31…

[andysouth]

Interesting @AnneMTreasure . So the object looks OK, but mapview doesn't like it.

Just checking that tmap works ?
tmap::tm_shape(afrihighway) + tm_lines()

Another route to try before the mapview command : library(rgdal)

[AnneMTreasure]

Hi @andysouth ,

tmap works:

tmap::tm_shape(afrihighway) + tm_lines()

I ran:

library(rgdal)

and reran:

mapview(afrihighway)

but still get this error:

Failed to create feature 0 in file2ba67b6ffdd3
Deleting layer not supported by driver `FlatGeobuf'
Error in CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  : 
  Feature creation failed.
In addition: Warning messages:
1: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 1: ICreateFeature: Mismatched geometry type
2: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 6: DeleteLayer() not supported by this dataset.

Are there any other packages I should have installed?

[andysouth]

Thanks @AnneMTreasure I think this is a mapview problem, maybe you/we can submit as an issue there.

One last thing to try. The kml file has a column that is mostly empty, which I filter out when creating the afrihighway object in afrilearndata. So could try this.

#remove Description column, only has contents in first row
afrihighway <- afrihighway[ , which(names(afrihighway)!='Description')]
mapview(afrihighway)

[AnneMTreasure]

Hi @andysouth ,

afrihighway <- afrihighway[ , which(names(afrihighway)!='Description')]
mapview(afrihighway)

still gives me:

Failed to create feature 0 in file2ba6758166f4
Deleting layer not supported by driver `FlatGeobuf'
Error in CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  : 
  Feature creation failed.
In addition: Warning messages:
1: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 1: ICreateFeature: Mismatched geometry type
2: In CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options),  :
  GDAL Error 6: DeleteLayer() not supported by this dataset.

[AnneMTreasure]

Hi @andysouth ,

Found this GitHub issue: mapview with FlatGeoBuf not rendering

I haven't read everything in that issue and the fixes that were used, but tried this one quickly:
Using:

mapviewOptions(fgb = FALSE)

before:

mapview(afrihighway)

and a map rendered. I'm not sure if this is what this map is supposed to look like:

For the online tutorial for intro to spatial data in R:

Section H. Read spatial data from files

The issue with rendering the plot appears here as well and I get the message:

Cannot create RasterLayer object from this file; perhaps you need to install rgdal first

I'm not sure if this helps?