Opened 5 years ago
Closed 20 months ago
#2145 closed defect (fixed)
R Jupyter demo errors
Reported by: | darkblueb | Owned by: | |
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Priority: | normal | Milestone: | OSGeoLive16.0 |
Component: | OSGeoLive | Keywords: | R, sf |
Cc: |
Description
Steps to reproduce:
- boot Live13 a2
- start the Jupyter system
- run the R Notebook
- execute each cell
library('sf') #SimpleFeature Library to handle shapefiles Linking to GEOS 3.7.0, GDAL 2.4.0, PROJ 5.2.0 Package: sf Version: 0.7-4 Title: Simple Features for R
The demo dot-shp file loads properly, but the first call to display data fails.
ERROR while rich displaying an object: Error in loadNamespace(name): there is no package called ‘geojsonio’ Traceback: 1. FUN(X[[i]], ...) 2. tryCatch(withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[[mime]](obj) . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler), error = outer_handler) 3. tryCatchList(expr, classes, parentenv, handlers) 4. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. doTryCatch(return(expr), name, parentenv, handler) 6. withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[[mime]](obj) . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler) 7. repr::mime2repr[[mime]](obj) 8. repr_geojson.sf(obj) 9. repr_geojson(geojsonio::geojson_list(obj), ...) 10. geojsonio::geojson_list 11. getExportedValue(pkg, name) 12. asNamespace(ns) 13. getNamespace(ns) 14. tryCatch(loadNamespace(name), error = function(e) stop(e)) 15. tryCatchList(expr, classes, parentenv, handlers) 16. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17. value[[3L]](cond)
An attempt to separately load geojsonio
fails in multiple ways
> install.packages('geojsonio') Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘hms’, ‘BH’, ‘protolite’, ‘rgdal’, ‘rgeos’, ‘maptools’, ‘readr’, ‘V8’, ‘geojson’, ‘jqr’ ... trying URL 'https://cloud.r-project.org/src/contrib/geojson_0.3.2.tar.gz' ... trying URL 'https://cloud.r-project.org/src/contrib/geojsonio_0.7.0.tar.gz' ...
Attachments (2)
Change History (17)
comment:1 by , 5 years ago
comment:2 by , 5 years ago
attaching two DEBUG logs, one from o12 (works), the second from o13 (fails)
duplicate of ticket #2134
by , 5 years ago
Attachment: | jupyter_ir_o13_debug.txt.bz2 added |
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by , 5 years ago
Attachment: | jupyter_ir_o12_debug.txt.bz2 added |
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comment:3 by , 5 years ago
previous comment by wildintellect
The cause is the IRKernel specifies that geojsonio package is used to display various things from sf objects. This is specific to Jupyter. Easiest solution is to add the geojsonio
R library and it's dependencies. Not sure how much space this will take. This does include need to add the system V8 library.
sudo apt-get install libv8-dev
https://github.com/IRkernel/repr/search?q=geojsonio&unscoped_q=geojsonio
comment:4 by , 5 years ago
Can you provide all the errors when trying to install geojsonio? That should tell us if any of the other packages are missing system libraries.
per the attached DEBUG logs, R modules rgdal
and rgeos
are not installed at all in the working osgeolive 12 final edition. It seems a bad indicator that rgdal
and rgeos
are being queued for install, as if this method of installation is wholly out of synch with the current setup.
comment:5 by , 5 years ago
osgeolive beta1 / sf 0.7-6 ; does draw, albeit with long warning text; sf team on the topic, will update status here
comment:6 by , 5 years ago
Priority: | critical → normal |
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comment:7 by , 5 years ago
Milestone: | OSGeoLive13.0 → OSGeoLive14.0 |
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Ticket retargeted after milestone closed
comment:8 by , 4 years ago
R sf osgeolive 14.0
Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.0
the above-mentioned geojson-io error msgs persists
comment:9 by , 4 years ago
Milestone: | OSGeoLive14.0 → OSGeoLive15.0 |
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Ticket retargeted after milestone closed
comment:11 by , 2 years ago
build 96 jupyter/notebook_gallery/R/R_spatial_introduction.ipynb
sids <- st_read(dsn = "/usr/lib/python3/dist-packages/pysal/lib/examples/sids2/sids2.shp" ) head(sids) ## ERROR while rich displaying an object: Error in loadNamespace(x): there is no package called ‘geojsonio’
the demo does draw using ggplot2
(small)
comment:12 by , 2 years ago
Summary: | R Jupyter demo Fails → R Jupyter demo errors |
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comment:13 by , 2 years ago
ol15 vmdk beta1
large warnings : "... there is no package called 'geojsonio' "
GEOS 3.10.2 GDAL 3.4.3 PROJ 8.2.1 sf_use_s2() is TRUE
comment:14 by , 2 years ago
Milestone: | OSGeoLive15.0 → OSGeoLive16.0 |
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Ticket retargeted after milestone closed
I looked into this a while back when you mentioned it. If I recall Jupyter has it's own code for printing/plotting which adds the geojsonio package dependency. From the initial list provided, V8 does have a system dependency of 'libv8-dev or libnode-dev'
Can you provide all the errors when trying to install geojsonio? That should tell us if any of the other packages are missing system libraries.