SoilGrid

[azam65]

I am working on SoilGrid and following this procedure,

https://envirometrix.github.io/PredictiveSoilMapping/software.html#Rstudio

session_info()

• Session info ---------------------------------------------------------------------------
  setting value
  version R version 3.5.3 (2019-03-11)
  os Windows >= 8 x64
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate English_United Kingdom.1252
  ctype English_United Kingdom.1252
  tz Asia/Taipei
  date 2019-04-23

• Packages -------------------------------------------------------------------------------
  ! package * version date lib source
  acepack 1.4.1 2016-10-29 [1] CRAN (R 3.5.2)
  aqp * 1.17 2019-01-03 [1] CRAN (R 3.5.2)
  V assertthat 0.2.0 2019-03-21 [1] CRAN (R 3.5.3)
  automap 1.0-14 2013-08-29 [1] CRAN (R 3.5.3)
  R backports 1.1.3 [1]
  base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.0)
  bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.1)
  bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.1)
  bitops 1.0-6 2013-08-17 [1] CRAN (R 3.5.0)
  V callr 3.1.1 2019-03-15 [1] CRAN (R 3.5.3)
  caret * 6.0-83 2019-04-18 [1] CRAN (R 3.5.3)
  R caTools 1.17.1.1 [1]
  checkmate 1.9.1 2019-01-15 [1] CRAN (R 3.5.2)
  class * 7.3-15 2019-01-01 [2] CRAN (R 3.5.3)
  classInt 0.3-1 2018-12-18 [1] CRAN (R 3.5.2)
  V cli 1.0.1 2019-03-19 [1] CRAN (R 3.5.3)
  cluster 2.0.7-1 2018-04-13 [2] CRAN (R 3.5.3)
  codetools 0.2-16 2018-12-24 [2] CRAN (R 3.5.3)
  colorRamps 2.3 2012-10-29 [1] CRAN (R 3.5.2)
  R colorspace * 1.4-0 [1]
  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
  curl 3.3 2019-01-10 [1] CRAN (R 3.5.2)
  R data.table 1.12.0 [1]
  DBI 1.0.0 2018-05-02 [1] CRAN (R 3.5.1)
  desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.2)
  R devtools * 2.0.1 [1]
  digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.1)
  dismo * 1.1-4 2017-01-09 [1] CRAN (R 3.5.2)
  doParallel * 1.0.14 2018-09-24 [1] CRAN (R 3.5.3)
  R dplyr 0.7.8 [1]
  R e1071 1.7-0.1 [1]
  evd 2.3-3 2018-04-25 [1] CRAN (R 3.5.3)
  fasterize * 1.0.0 2018-03-22 [1] CRAN (R 3.5.3)
  FNN 1.1.3 2019-02-15 [1] CRAN (R 3.5.2)
  foreach * 1.4.4 2017-12-12 [1] CRAN (R 3.5.3)
  foreign 0.8-71 2018-07-20 [2] CRAN (R 3.5.3)
  Formula * 1.2-3 2018-05-03 [1] CRAN (R 3.5.2)
  R fs 1.2.6 [1]
  gam * 1.16 2018-07-20 [1] CRAN (R 3.5.3)
  gdata 2.18.0 2017-06-06 [1] CRAN (R 3.5.2)
  generics 0.0.2 2018-11-29 [1] CRAN (R 3.5.2)
  V ggplot2 * 3.1.0 2019-04-07 [1] CRAN (R 3.5.3)
  ggRandomForests * 2.0.1 2016-09-07 [1] CRAN (R 3.5.3)
  glmnet * 2.0-16 2018-04-02 [1] CRAN (R 3.5.3)
  R glue 1.3.0 [1]
  gower 0.2.0 2019-03-07 [1] CRAN (R 3.5.3)
  gplots * 3.0.1.1 2019-01-27 [1] CRAN (R 3.5.3)
  gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.2)
  GSIF * 0.5-5 2019-01-04 [1] CRAN (R 3.5.2)
  R gstat 1.1-6 [1]
  V gtable 0.2.0 2019-03-25 [1] CRAN (R 3.5.3)
  gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.2)
  h2o * 3.22.1.1 2019-01-10 [1] CRAN (R 3.5.3)
  h2oEnsemble * 0.2.1 2019-04-23 [1] local
  hexbin * 1.27.2 2018-01-15 [1] CRAN (R 3.5.1)
  Hmisc * 4.2-0 2019-01-26 [1] CRAN (R 3.5.2)
  htmlTable 1.13.1 2019-01-07 [1] CRAN (R 3.5.2)
  htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
  htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.1)
  intamap * 1.4-9 2018-05-02 [1] CRAN (R 3.5.3)
  intervals 0.15.1 2015-08-27 [1] CRAN (R 3.5.2)
  ipred 0.9-8 2018-11-05 [1] CRAN (R 3.5.3)
  iterators * 1.0.10 2018-07-13 [1] CRAN (R 3.5.3)
  jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.2)
  KernSmooth 2.23-15 2015-06-29 [2] CRAN (R 3.5.3)
  R knitr 1.21 [1]
  R lattice * 0.20-38 [2]
  latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.5.2)
  lava 1.6.5 2019-02-12 [1] CRAN (R 3.5.3)
  R lazyeval 0.2.1 [1]
  lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.5.1)
  magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.2)
  MASS 7.3-51.1 2018-11-01 [2] CRAN (R 3.5.3)
  Matrix * 1.2-15 2018-11-01 [2] CRAN (R 3.5.3)
  matrixStats * 0.54.0 2018-07-23 [1] CRAN (R 3.5.3)
  mda * 0.4-10 2017-11-02 [1] CRAN (R 3.5.3)
  memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.2)
  mnormt 1.5-5 2016-10-15 [1] CRAN (R 3.5.2)
  ModelMetrics 1.2.2 2018-11-03 [1] CRAN (R 3.5.3)
  munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
  R mvtnorm 1.0-8 [1]
  nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.3)
  nnet * 7.3-12 2016-02-02 [2] CRAN (R 3.5.3)
  nnls * 1.4 2012-03-19 [1] CRAN (R 3.5.2)
  pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.2)
  pixmap 0.4-11 2011-07-19 [1] CRAN (R 3.5.2)
  V pkgbuild 1.0.2 2019-03-20 [1] CRAN (R 3.5.3)
  pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1)
  pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.2)
  plotKML * 0.5-9 2019-01-09 [1] CRAN (R 3.5.2)
  V plotrix 3.7-4 2019-04-07 [1] CRAN (R 3.5.3)
  plyr * 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
  prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
  R processx 3.2.1 [1]
  prodlim 2018.04.18 2018-04-18 [1] CRAN (R 3.5.3)
  ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.2)
  psych * 1.8.12 2019-01-12 [1] CRAN (R 3.5.2)
  R purrr 0.3.0 [1]
  quantregForest * 1.3-7 2017-12-19 [1] CRAN (R 3.5.3)
  V R6 2.3.0 2019-02-14 [1] CRAN (R 3.5.3)
  randomForest * 4.6-14 2018-03-25 [1] CRAN (R 3.5.3)
  R randomForestSRC * 2.8.0 [1]
  ranger * 0.11.2 2019-03-07 [1] CRAN (R 3.5.3)
  raster * 2.8-19 2019-01-30 [1] CRAN (R 3.5.2)
  RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 3.5.2)
  R Rcpp 1.0.0 [1]
  R RCurl 1.95-4.11 [1]
  recipes 0.1.5 2019-03-21 [1] CRAN (R 3.5.3)
  V remotes 2.0.2 2019-04-10 [1] CRAN (R 3.5.3)
  reshape * 0.8.8 2018-10-23 [1] CRAN (R 3.5.3)
  reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.3)
  R rgdal * 1.3-6 [1]
  D rJava * 0.9-11 2019-03-29 [1] CRAN (R 3.5.3)
  R rlang 0.3.1 [1]
  ROCR * 1.0-7 2015-03-26 [1] CRAN (R 3.5.3)
  rpart 4.1-13 2018-02-23 [2] CRAN (R 3.5.3)
  rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
  RSAGA 1.3.0 2018-11-12 [1] CRAN (R 3.5.2)
  V rstudioapi 0.9.0 2019-03-19 [1] CRAN (R 3.5.3)
  scales * 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
  sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.2)
  shapefiles 0.7 2013-01-26 [1] CRAN (R 3.5.2)
  snow * 0.4-3 2018-09-14 [1] CRAN (R 3.5.2)
  snowfall * 1.84-6.1 2015-10-14 [1] CRAN (R 3.5.2)
  soiltexture * 1.5.1 2018-09-20 [1] CRAN (R 3.5.2)
  sp * 1.3-1 2018-06-05 [1] CRAN (R 3.5.1)
  spacetime 1.2-2 2018-07-17 [1] CRAN (R 3.5.2)
  R stringi 1.2.4 [1]
  V stringr 1.3.1 2019-02-10 [1] CRAN (R 3.5.3)
  SuperLearner * 2.0-24 2018-08-11 [1] CRAN (R 3.5.3)
  survival * 2.43-3 2018-11-26 [2] CRAN (R 3.5.3)
  R tibble 2.0.1 [1]
  R tidyr 0.8.2 [1]
  tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1)
  timeDate 3043.102 2018-02-21 [1] CRAN (R 3.5.2)
  units 0.6-2 2018-12-05 [1] CRAN (R 3.5.2)
  R usethis * 1.4.0 [1]
  viridis * 0.5.1 2018-03-29 [1] CRAN (R 3.5.1)
  viridisLite * 0.3.0 2018-02-01 [1] CRAN (R 3.5.1)
  withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
  V xfun 0.4 2019-04-02 [1] CRAN (R 3.5.3)
  xgboost * 0.82.1 2019-03-11 [1] CRAN (R 3.5.3)
  R XML 3.98-1.17 [1]
  xts 0.11-2 2018-11-05 [1] CRAN (R 3.5.2)
  R zoo 1.8-4 [1]

[1] D:/UserData/My Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.3/library

V -- Loaded and on-disk version mismatch.
D -- DLL MD5 mismatch, broken installation.
R -- Package was removed from disk.

I got this error,
om.rk
Variable : om
Minium value : 1
Maximum value : 17
Size : 153
Error in plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
lazy-load database 'D:/UserData/My Documents/R/win-library/3.5/stringr/R/stringr.rdb' is corrupt
In addition: Warning messages:
1: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
restarting interrupted promise evaluation
2: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
internal error -3 in R_decompress1
Error in new("standardGeneric", .Data = function (object) :
object 'prj' not found

plotKML(om.rk)
Error in plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
lazy-load database 'D:/UserData/My Documents/R/win-library/3.5/stringr/R/stringr.rdb' is corrupt
In addition: Warning messages:
1: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
restarting interrupted promise evaluation
2: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
internal error -3 in R_decompress1
Error in .local(object, ...) : object 'prj' not found

[thengl]

The error reports problem with the "stringr" package. Try removing it and reinstalling it from https://cran.r-project.org/package=stringr
I've just tested the code by using:

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
> packageDescription("stringr")
Package: stringr
Title: Simple, Consistent Wrappers for Common String Operations
Version: 1.4.0

and runs fine.

[azam65]

thanks , as you suggested I just reinstalled stringr package.