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SoilGrid #11

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azam65 opened this issue Apr 23, 2019 · 2 comments
Open

SoilGrid #11

azam65 opened this issue Apr 23, 2019 · 2 comments
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@thengl
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help wanted Extra attention is needed

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@azam65
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azam65 commented Apr 23, 2019

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
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thengl commented Apr 23, 2019

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.

@thengl thengl added the help wanted Extra attention is needed label Apr 23, 2019
@thengl thengl self-assigned this Apr 23, 2019
@azam65
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azam65 commented Apr 25, 2019

thanks , as you suggested I just reinstalled stringr package.

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@thengl @azam65