#2145: R Jupyter demo Fails

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#2145: R Jupyter demo Fails

OSGeoLive
#2145: R Jupyter demo Fails
-----------------------+---------------------------
 Reporter:  darkblueb  |      Owner:  osgeolive@…
     Type:  defect     |     Status:  new
 Priority:  critical   |  Milestone:  OSGeoLive13.0
Component:  OSGeoLive  |   Keywords:  R, sf
-----------------------+---------------------------
 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'
 ...
 }}}

--
Ticket URL: <https://trac.osgeo.org/osgeolive/ticket/2145>
OSGeoLive <http://live.osgeo.org/>
self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.

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Re: #2145: R Jupyter demo Fails

OSGeoLive
#2145: R Jupyter demo Fails
-----------------------+----------------------------
 Reporter:  darkblueb  |       Owner:  osgeolive@…
     Type:  defect     |      Status:  new
 Priority:  critical   |   Milestone:  OSGeoLive13.0
Component:  OSGeoLive  |  Resolution:
 Keywords:  R, sf      |
-----------------------+----------------------------

Comment (by wildintellect):

 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.

--
Ticket URL: <https://trac.osgeo.org/osgeolive/ticket/2145#comment:1>
OSGeoLive <http://live.osgeo.org/>
self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.

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Re: #2145: R Jupyter demo Fails

OSGeoLive
In reply to this post by OSGeoLive
#2145: R Jupyter demo Fails
-----------------------+----------------------------
 Reporter:  darkblueb  |       Owner:  osgeolive@…
     Type:  defect     |      Status:  new
 Priority:  critical   |   Milestone:  OSGeoLive13.0
Component:  OSGeoLive  |  Resolution:
 Keywords:  R, sf      |
-----------------------+----------------------------

Comment (by darkblueb):

 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

--
Ticket URL: <https://trac.osgeo.org/osgeolive/ticket/2145#comment:3>
OSGeoLive <http://live.osgeo.org/>
self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.

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Re: #2145: R Jupyter demo Fails

OSGeoLive
In reply to this post by OSGeoLive
#2145: R Jupyter demo Fails
-----------------------+----------------------------
 Reporter:  darkblueb  |       Owner:  osgeolive@…
     Type:  defect     |      Status:  new
 Priority:  critical   |   Milestone:  OSGeoLive13.0
Component:  OSGeoLive  |  Resolution:
 Keywords:  R, sf      |
-----------------------+----------------------------

Comment (by darkblueb):

 ''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.

--
Ticket URL: <https://trac.osgeo.org/osgeolive/ticket/2145#comment:4>
OSGeoLive <http://live.osgeo.org/>
self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.

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Re: #2145: R Jupyter demo Fails

OSGeoLive
In reply to this post by OSGeoLive
#2145: R Jupyter demo Fails
-----------------------+----------------------------
 Reporter:  darkblueb  |       Owner:  osgeolive@…
     Type:  defect     |      Status:  new
 Priority:  critical   |   Milestone:  OSGeoLive13.0
Component:  OSGeoLive  |  Resolution:
 Keywords:  R, sf      |
-----------------------+----------------------------

Comment (by darkblueb):

 osgeolive beta1 / **sf** 0.7-6  ;  does draw, albeit with long warning
 text; **sf** team on the topic, will update status here

--
Ticket URL: <https://trac.osgeo.org/osgeolive/ticket/2145#comment:5>
OSGeoLive <http://live.osgeo.org/>
self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.

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