geopandas.read_file() works in R session but crashes shiny session

[leungi]

Scenario

• use reticulate to import geopandas to read a .shp file
• works in R session within machine where shiny server sits, but fails when run as shiny server app

R session

[leungi@shiny]$ R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> wd <- "/opt/shiny-server/samples/sample-apps/my_project"
> sections_path <- "/Data/NM.shp"
> gpd = import("geopandas")
> shp_dat <- gpd$read_file(file.path(wd, sections_path))
> head(shp_dat)
  STATE COUNTY MERIDIAN TWP TDIR RNG RDIR SECT STCTY MAINT__ID OBJECT__ID
1    30      5       23  16    S  16    E   31 30005   2236037    1561107
2    30      5       23  18    S  16    E   30 30005   2260363    1564838
3    30      5       23  19    S  16    E    7 30005   2267140    1565939
4    30      5       23  19    S  16    E    6 30005   2264997    1565610
5    30      5       23  19    S  16    E   30 30005   2273561    1566964
6    30      5       23  16    S  16    E    8 30005   2227246    1559742
       SNAME  CNAME   SHAPE_AREA  SHAPE_LEN                 geometry
1 NEW MEXICO CHAVES 0.0001942569 0.05635857 <environment: 0x75a6d78>
2 NEW MEXICO CHAVES 0.0002301894 0.06074057 <environment: 0x75b19b8>
3 NEW MEXICO CHAVES 0.0002448596 0.06278105 <environment: 0x75ba870>
4 NEW MEXICO CHAVES 0.0002492395 0.06340133 <environment: 0x75c54e8>
5 NEW MEXICO CHAVES 0.0002513312 0.06353639 <environment: 0x75cc368>
6 NEW MEXICO CHAVES 0.0002524851 0.06380171 <environment: 0x75d9018>

Sessioninfo

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] reticulate_1.12

loaded via a namespace (and not attached):
[1] compiler_3.6.0  Matrix_1.2-17   Rcpp_1.0.1      grid_3.6.0
[5] jsonlite_1.6    lattice_0.20-38

Shiny app /var/log/

Listening on http://127.0.0.1:44147
R: geos_ts_c.cpp:3472: int GEOSCoordSeq_setOrdinate_r(GEOSContextHandle_t, geos::geom::CoordinateSequence*, unsigned int, unsigned int, double): Assertion `0 != cs' failed.
-bash: line 1: 58500 Aborted                 (core dumped) R --no-save --slave -f \/opt\/shiny-server\/R\/SockJSAdapter\.R

[leungi]

Painful debugging experience, but found the solution/issue.

Don't load rgdal explicitly with library() when working with geospatial related Python libraries such as:

• rasterio
• geopandas
• rasterstats

The reason rgdal was needed was to plot the shapefile output of Python code, and rgdal::readOGR() was used to read in file.