Open anelda opened 3 years ago
andysouth
commented
3 years ago 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
commented
3 years ago 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
commented
3 years ago Thanks @anelda @AnneMTreasure, this one should be fixed by 083e2e02e402a36bcbf246a171cb08213a11803d Can you reinstall & try again ? Thanks.
AnneMTreasure
commented
3 years ago 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
commented
3 years ago 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
commented
3 years ago 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
commented
3 years ago 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.Thanks @AnneMTreasure seems to be a problem with either reading in or plotting the highways.
Can you try : str(afrihighway) head(afrihighway)
AnneMTreasure
commented
3 years ago 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…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
commented
3 years ago 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
commented
3 years ago 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.
afrihighway <- afrihighway[ , which(names(afrihighway)!='Description')] mapview(afrihighway)
AnneMTreasure
commented
3 years ago 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.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?
andysouth
commented
3 years ago Thanks @AnneMTreasure, good google work finding the FlatGeoBuf error 👍 . I saw that but didn't get as far as you in actually trying it. This is what makes me think this is a mapview problem and not ours. Can you just install latest version of mapview and check the error persists ? If so, can you submit this reproducible example as an issue to mapview ? That way the developers can test it at their end. Better coming from you given that it doesn't seem to happen on my windows machine.
remotes::install_github('afrimapr/afrilearndata')
library(afrilearndata)
mapview(afrihighway)Re the other problem, better to submit that here as a separate issue. There's a chance it might be fixed by a recent commit I've made (fingers crossed).
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")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