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Envirometrix / landmap

Landmap package for R
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landmap demo failing with error `rvgm not found` #2

Closed barryrowlingson closed 3 years ago

barryrowlingson commented 5 years ago

Transcript:

> library(rgdal)
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
> library(geoR)
'RandomFieldsUtils' will use OMP
'RandomFields' will use OMP
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2.1 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

> library(plotKML)
plotKML version 0.5-9 (2019-01-04)
URL: http://plotkml.r-forge.r-project.org/
> library(raster)
> library(SuperLearner)
Loading required package: nnls
Super Learner
Version: 2.0-24
Package created on 2018-08-10

> library(subsemble)
subsemble (beta)
Version: 0.0.9.9000
Package created on 2014-12-09

Notice to subsemble users:
The interface (function arguments/values) may be subject to change prior to version 1.0.0.
> demo(meuse, echo=FALSE)
> m <- train.spLearner(meuse["lead"], covariates=meuse.grid[,c("dist","ffreq")], lambda = 1)
Error in train.spLearner(meuse["lead"], covariates = meuse.grid[, c("dist",  : 
  could not find function "train.spLearner"
> library(landmap)
> demo(meuse, echo=FALSE)
> m <- train.spLearner(meuse["lead"], covariates=meuse.grid[,c("dist","ffreq")], lambda = 1)
Converting ffreq to indicators...
Converting covariates to principal components...
Deriving buffer distances to points...TRUE
Error in .solve.geoR(crossprod(xmat)) : 
  Singular matrix. Covariates may have different orders of magnitude.
In addition: Warning message:
In sqrt(t.ei$val) : NaNs produced
Fitting a variogram using 'linkfit' and trend model...TRUE
Error in c("practicalRange", "cov.model") %in% names(rvgm) : 
  object 'rvgm' not found

and session info:


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /nobackup/rowlings/Downloads/R-3.5.1/lib/libRblas.so
LAPACK: /nobackup/rowlings/Downloads/R-3.5.1/lib/libRlapack.so

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

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

other attached packages:
[1] landmap_0.0.0.9000   subsemble_0.0.9.9000 SuperLearner_2.0-24 
[4] nnls_1.4             raster_2.9-5         plotKML_0.5-9       
[7] geoR_1.7-5.2.1       rgdal_1.4-3          sp_1.3-1            

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1              lattice_0.20-35         FNN_1.1.3              
 [4] class_7.3-14            zoo_1.8-6               gstat_2.0-2            
 [7] digest_0.6.19           plyr_1.8.4              RandomFields_3.3.6     
[10] backports_1.1.4         acepack_1.4.1           e1071_1.7-1            
[13] ggplot2_3.1.1           pillar_1.4.1            rlang_0.3.4            
[16] lazyeval_0.2.2          data.table_1.12.2       rstudioapi_0.10        
[19] rpart_4.1-13            Matrix_1.2-14           checkmate_1.9.3        
[22] splines_3.5.1           stringr_1.4.0           foreign_0.8-70         
[25] htmlwidgets_1.3         munsell_0.5.0           xfun_0.7               
[28] compiler_3.5.1          shapefiles_0.7          pkgconfig_2.0.2        
[31] dismo_1.1-4             base64enc_0.1-3         aqp_1.17               
[34] htmltools_0.3.6         tcltk_3.5.1             nnet_7.3-12            
[37] tibble_2.1.1            gridExtra_2.3           htmlTable_1.13.1       
[40] intervals_0.15.1        Hmisc_4.2-0             codetools_0.2-15       
[43] XML_3.98-1.19           reshape_0.8.8           spacetime_1.2-2        
[46] crayon_1.3.4            MASS_7.3-50             grid_3.5.1             
[49] gtable_0.3.0            RSAGA_1.3.0             magrittr_1.5           
[52] scales_1.0.0            stringi_1.4.3           pixmap_0.4-11          
[55] latticeExtra_0.6-28     colorRamps_2.3          xts_0.11-2             
[58] Formula_1.2-3           RColorBrewer_1.1-2      tools_3.5.1            
[61] splancs_2.01-40         parallel_3.5.1          plotrix_3.7-5          
[64] survival_2.42-3         colorspace_1.4-1        cluster_2.0.7-1        
[67] classInt_0.3-1          knitr_1.23              RandomFieldsUtils_0.5.3