- using R version 4.3.3 (2024-02-29 ucrt)
- using platform: x86_64-w64-mingw32 (64-bit)
- R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'smile/DESCRIPTION' ... OK
- this is package 'smile' version '1.0.4.1'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'smile' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 12.3.0'
- checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
- checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 4.6Mb
libs 1.1Mb
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s] OK
- checking whether the package can be unloaded cleanly ... [2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [11s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... [2s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [7s] ERROR
Running examples in 'smile-Ex.R' failed
The error most likely occurred in:
> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ### points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
>
> ### ** Examples
>
>
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
>
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+ type = "regular", by_polygon = FALSE,
+ poly_ids = "msoa11cd",
+ var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
>
> fit_msoa <-
+ fit_spm(x = msoa_spm,
+ theta_st = theta_st_msoa,
+ model = "matern",
+ nu = .5,
+ apply_exp = TRUE,
+ opt_method = "L-BFGS-B",
+ control = list(maxit = 500))
>
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [29s] ERROR
Error(s) in re-building vignettes:
--- re-building 'fit-and-pred.Rmd' using rmarkdown
Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building 'fit-and-pred.Rmd'
--- re-building 'sai.Rmd' using rmarkdown
--- finished re-building 'sai.Rmd'
--- re-building 'sf-to-spm.Rmd' using rmarkdown
Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building 'sf-to-spm.Rmd'
--- re-building 'sp-cov-functions.Rmd' using rmarkdown
--- finished re-building 'sp-cov-functions.Rmd'
--- re-building 'theory.Rmd' using rmarkdown
--- finished re-building 'theory.Rmd'
SUMMARY: processing the following files failed:
'fit-and-pred.Rmd' 'sf-to-spm.Rmd'
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [19s] OK
- checking HTML version of manual ... [12s] OK
- DONE
Status: 2 ERRORs, 2 NOTEs