* using log directory ‘/Users/ripley/R/packages/tests-devel/smile.Rcheck’
* using R Under development (unstable) (2024-04-06 r86349)
* using platform: aarch64-apple-darwin23.4.0
* R was compiled by
    Apple clang version 15.0.0 (clang-1500.3.9.4)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.4.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘smile’ can be installed ... [10s/11s] OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
* used SDK: ‘MacOSX14.4.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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 compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘fit-and-pred.Rmd’ using rmarkdown

Quitting from lines  at 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  at 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 ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/Users/ripley/R/packages/tests-devel/smile.Rcheck/00check.log’
for details.

       43.73 real        37.70 user         4.44 sys