GDAL Erorr 4: Unable to open EPSG support file gcs.csv.

[erstearns]

I have a Shiny app that sets the crs of sf objects. This has been running fine until I pushed to the shinyio server as well as an AWS Linux server where I encountered the following error: Warning: Error in CPL_transform: OGR error. I went into the code to check the error on my local machine, running Ubuntu 18.04.3 (further system details below) and now my Shiny app does not work locally either and I am running into the following error after running st_transform on an sf object(
state_bounds <- st_transform(state_bounds, crs = 4326)):

Warning in CPL_crs_from_epsg(as.integer(x)) : GDAL Error 4: Unable to open EPSG support file gcs.csv. Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files. OGR: Corrupt data Error in CPL_transform(x, crs$proj4string) : OGR error

I set the GDAL_DATA environment variable and still received the same error.

I then re-installed RGDAL, and sf and ran into this error pertaining to a tmap call in a downloadable report (.Rmd) file:

Warning: Error in : package or namespace load failed for 'tmap' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/e/Dropbox/R_lib/3.6/lwgeom/libs/lwgeom.so':
  libproj.so.13: cannot open shared object file: No such file or directory
  [No stack trace available]

When I try to check my versions of geospatial libraries, GEOS and GDAL return version info (see below) but PROJ returns the following:

Rel. 6.2.1, November 1st, 2019
<proj>: 
projection initialization failure
cause: no arguments in initialization list
program abnormally terminated

I am truly bamboozled by this sequence of events because I literally changed nothing from yesterday and everything ran great. My questions are:

1. Has there been some sort of update to any packages or libraries in the past 24 hours that would somehow auto-install?
2. What is the best path forward to resolving this issue?

Thank you in advance for your help.

Geospatial libraries version information:
GDAL version: GDAL 3.0.2, released 2019/10/28
GEOS version: 3.8.0

Session information:

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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] forcats_0.4.0        purrr_0.3.3          readr_1.3.1         
 [4] tidyr_1.0.0          tibble_2.1.3         tidyverse_1.2.1     
 [7] scales_1.0.0         rmarkdown_1.16       DT_0.9              
[10] png_0.1-7            RColorBrewer_1.1-2   plotly_4.9.0.9000   
[13] ggplot2_3.2.1        leaflet.extras_1.0.0 leaflet_2.0.2       
[16] data.table_1.12.6    dplyr_0.8.3          gstat_2.0-3         
[19] raster_3.0-7         sf_0.8-0             rgdal_1.4-8         
[22] sp_1.3-1             stringr_1.4.0        V8_2.3              
[25] shinyWidgets_0.4.9   rintrojs_0.2.2       shinyjs_1.0         
[28] reactlog_1.0.0       shiny_1.4.0         

loaded via a namespace (and not attached):
 [1] nlme_3.1-142       xts_0.11-2         lubridate_1.7.4   
 [4] httr_1.4.1         tools_3.6.1        backports_1.1.5   
 [7] R6_2.4.0           KernSmooth_2.23-16 DBI_1.0.0         
[10] lazyeval_0.2.2     colorspace_1.4-1   withr_2.1.2       
[13] tidyselect_0.2.5   curl_4.2           compiler_3.6.1    
[16] cli_1.1.0          rvest_0.3.4        xml2_1.2.2        
[19] labeling_0.3       classInt_0.4-1     askpass_1.1       
[22] digest_0.6.22      dichromat_2.0-0    pkgconfig_2.0.3   
[25] htmltools_0.4.0    fastmap_1.0.1      readxl_1.3.1      
[28] htmlwidgets_1.5.1  rlang_0.4.1        rstudioapi_0.10   
[31] FNN_1.1.3          generics_0.0.2     zoo_1.8-6         
[34] jsonlite_1.6       crosstalk_1.0.0    magrittr_1.5      
[37] Rcpp_1.0.2         munsell_0.5.0      lifecycle_0.1.0   
[40] leafsync_0.1.0     stringi_1.4.3      yaml_2.2.0        
[43] grid_3.6.1         promises_1.1.0     crayon_1.3.4      
[46] fortunes_1.5-4     lattice_0.20-38    haven_2.1.1       
[49] hms_0.5.1          zeallot_0.1.0      knitr_1.25        
[52] pillar_1.4.2       spacetime_1.2-2    codetools_0.2-16  
[55] XML_3.98-1.20      glue_1.3.1         packrat_0.5.0     
[58] evaluate_0.14      modelr_0.1.5       vctrs_0.2.0       
[61] httpuv_1.5.2       cellranger_1.1.0   gtable_0.3.0      
[64] openssl_1.4.1      assertthat_0.2.1   xfun_0.10         
[67] mime_0.7           xtable_1.8-4       broom_0.5.2       
[70] e1071_1.7-2        later_1.0.0        rsconnect_0.8.15  
[73] class_7.3-15       viridisLite_0.3.0  intervals_0.15.1  
[76] units_0.6-5   

[edzer]

On your system, several R packages (rgdal, sf, lwgeom) link to external libraries (GDAL, GEOS and/or PROJ). It sounds like (some of) these libraries were updated after installing the R packages, and at that point you often need to reinstall the R packages involved. Have you tried reinstalling lwgeom?

[Robinlovelace]

Heads-up I just hit this issue after updating GDAL on my system. Details to follow in case it's of use to others...

[Robinlovelace]

Reprex showing my set-up below. Next step: try re-installing the packages as suggested...:

library(sf)
#> Linking to GEOS 3.8.0, GDAL 2.4.2, PROJ 5.2.0
#> WARNING: different compile-time and runtime versions for GEOS found:
#> Linked against: 3.8.0-CAPI-1.13.1  compiled against: 3.7.1-CAPI-1.11.1
#> It is probably a good idea to reinstall sf, and maybe rgeos and rgdal too
library(spData)
data("us_states", package = "spData")
north_carolina = read_sf(system.file("shape/nc.shp", package = "sf"))
#> Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet, : GDAL
#> Error 4: Unable to open EPSG support file gcs.csv. Try setting the GDAL_DATA
#> environment variable to point to the directory containing EPSG csv files.
us_states_2163 = st_transform(us_states, crs = 2163)
#> Warning in CPL_crs_from_epsg(as.integer(x)): GDAL Error 4: Unable to open EPSG
#> support file gcs.csv. Try setting the GDAL_DATA environment variable to point to
#> the directory containing EPSG csv files.
#> OGR: Corrupt data
#> Error in CPL_transform(x, crs$proj4string): OGR error
north_carolina_2163 = st_transform(north_carolina, crs = 2163)
#> Warning in CPL_crs_from_epsg(as.integer(x)): GDAL Error 4: Unable to open EPSG
#> support file gcs.csv. Try setting the GDAL_DATA environment variable to point to
#> the directory containing EPSG csv files.
#> OGR: Corrupt data
#> Error in CPL_transform(x, crs$proj4string): OGR error

^{Created on 2019-12-06 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.1 (2019-07-05)
#>  os       Ubuntu 18.04.3 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/London               
#>  date     2019-12-06                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source                              
#>  assertthat    0.2.1   2019-03-21 [2] CRAN (R 3.6.0)                      
#>  backports     1.1.5   2019-10-02 [1] CRAN (R 3.6.1)                      
#>  callr         3.3.2   2019-09-22 [1] CRAN (R 3.6.1)                      
#>  class         7.3-15  2019-01-01 [2] standard (@7.3-15)                  
#>  classInt      0.4-3   2019-12-04 [1] Github (r-spatial/classInt@7bc8a82) 
#>  cli           1.1.0   2019-03-19 [2] CRAN (R 3.5.3)                      
#>  crayon        1.3.4   2017-09-16 [2] standard (@1.3.4)                   
#>  DBI           1.0.0   2018-05-02 [2] CRAN (R 3.5.2)                      
#>  desc          1.2.0   2018-05-01 [2] standard (@1.2.0)                   
#>  devtools      2.2.1   2019-09-24 [1] CRAN (R 3.6.1)                      
#>  digest        0.6.23  2019-11-23 [1] CRAN (R 3.6.1)                      
#>  e1071         1.7-3   2019-11-26 [2] CRAN (R 3.6.1)                      
#>  ellipsis      0.3.0   2019-09-20 [1] CRAN (R 3.6.1)                      
#>  evaluate      0.14    2019-05-28 [2] CRAN (R 3.6.0)                      
#>  fs            1.3.1   2019-05-06 [2] CRAN (R 3.6.0)                      
#>  glue          1.3.1   2019-03-12 [2] CRAN (R 3.5.3)                      
#>  highr         0.8     2019-03-20 [3] CRAN (R 3.5.3)                      
#>  htmltools     0.4.0   2019-10-04 [3] CRAN (R 3.6.1)                      
#>  KernSmooth    2.23-16 2019-10-15 [4] CRAN (R 3.6.1)                      
#>  knitr         1.26    2019-11-12 [1] CRAN (R 3.6.1)                      
#>  magrittr      1.5     2014-11-22 [2] CRAN (R 3.5.2)                      
#>  memoise       1.1.0   2017-04-21 [3] CRAN (R 3.5.0)                      
#>  pillar        1.4.2   2019-06-29 [2] CRAN (R 3.6.0)                      
#>  pkgbuild      1.0.6   2019-10-09 [2] CRAN (R 3.6.1)                      
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 3.6.1)                      
#>  pkgload       1.0.2   2018-10-29 [3] CRAN (R 3.5.1)                      
#>  prettyunits   1.0.2   2015-07-13 [2] CRAN (R 3.5.3)                      
#>  processx      3.4.1   2019-07-18 [2] CRAN (R 3.6.1)                      
#>  ps            1.3.0   2018-12-21 [2] CRAN (R 3.5.3)                      
#>  R6            2.4.1   2019-11-12 [1] CRAN (R 3.6.1)                      
#>  Rcpp          1.0.3   2019-11-08 [1] CRAN (R 3.6.1)                      
#>  remotes       2.1.0   2019-06-24 [1] CRAN (R 3.6.1)                      
#>  rlang         0.4.2   2019-11-23 [1] CRAN (R 3.6.1)                      
#>  rmarkdown     1.18    2019-11-27 [1] CRAN (R 3.6.1)                      
#>  rprojroot     1.3-2   2018-01-03 [2] CRAN (R 3.5.3)                      
#>  sessioninfo   1.1.1   2018-11-05 [3] CRAN (R 3.5.1)                      
#>  sf          * 0.8-0   2019-09-17 [1] CRAN (R 3.6.1)                      
#>  spData      * 0.3.2   2019-09-19 [1] CRAN (R 3.6.1)                      
#>  spDataLarge   0.3.1   2019-05-29 [2] Github (nowosad/spDataLarge@012fe53)
#>  stringi       1.4.3   2019-03-12 [2] CRAN (R 3.5.3)                      
#>  stringr       1.4.0   2019-02-10 [2] standard (@1.4.0)                   
#>  testthat      2.3.0   2019-11-05 [2] CRAN (R 3.6.1)                      
#>  tibble        2.1.3   2019-06-06 [2] CRAN (R 3.6.0)                      
#>  units         0.6-5   2019-10-08 [1] CRAN (R 3.6.1)                      
#>  usethis       1.5.1   2019-07-04 [1] CRAN (R 3.6.1)                      
#>  withr         2.1.2   2018-03-15 [2] CRAN (R 3.5.3)                      
#>  xfun          0.11    2019-11-12 [1] CRAN (R 3.6.1)                      
#>  yaml          2.2.0   2018-07-25 [3] CRAN (R 3.5.1)                      
#> 
#> [1] /home/robin/R/x86_64-pc-linux-gnu-library/3.6
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

[Robinlovelace]

Updating all the relevant packages with:

remotes::install_cran("sf", force = TRUE)
remotes::install_cran("rgdal", force = TRUE)
remotes::install_cran("rgeos", force = TRUE)
remotes::install_cran("lwgeom", force = TRUE)

[Robinlovelace]

Good news: after re-installing those packages, it works! Thanks for reporting the issue @erstearns and the quickfire info on how to fix it.

library(sf)
#> Linking to GEOS 3.8.0, GDAL 3.0.2, PROJ 6.2.1
library(spData)
data("us_states", package = "spData")
north_carolina = read_sf(system.file("shape/nc.shp", package = "sf"))
us_states_2163 = st_transform(us_states, crs = 2163)
north_carolina_2163 = st_transform(north_carolina, crs = 2163)

^{Created on 2019-12-06 by the reprex package (v0.3.0)}

[edzer]

@Robinlovelace which OS & version is this?

[Robinlovelace]

See the details in the session info above:

[Robinlovelace]

Ubuntu, same as @erstearns by the looks of it. Auto update from ubuntugis-unstable:

egrep -v '^#|^ *$' /etc/apt/sources.list /etc/apt/sources.list.d/* | grep gis
/etc/apt/sources.list:deb https://qgis.org/ubuntugis bionic main
/etc/apt/sources.list:deb-src https://qgis.org/ubuntugis bionic main
/etc/apt/sources.list.d/ubuntugis-ubuntu-ubuntugis-unstable-bionic.list:deb http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu bionic main
/etc/apt/sources.list.d/ubuntugis-ubuntu-ubuntugis-unstable-bionic.list.save:deb http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu bionic main

[edzer]

Thanks; so Ubuntu LTS with PPA ubuntugis-unstable (our recommended r-spatial Ubuntu platform) is now on GDAL 3.0.2 and PROJ 6.2.1. Also relevant for r-spatial/discuss#28 and #1033

[erstearns]

Woohoo! Thank you @edzer and @Robinlovelace ! My app is alive and well again :) Thank you for your swift problem-solving and help with this!