- using R Under development (unstable) (2024-03-25 r86189)
- using platform: x86_64-pc-linux-gnu
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clang version 18.1.2
flang-new version 18.1.2
- running under: Fedora Linux 36 (Workstation Edition)
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- this is package ‘smile’ version ‘1.0.4.1’
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- checking whether package ‘smile’ can be installed ... [90s/86s] OK
See the install log for details.
- used C++ compiler: ‘clang version 18.1.2’
- 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
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- checking R code for possible problems ... [25s/27s] 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
| ^
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Documented arguments not in \usage in Rd file 'aux_cs.Rd':
‘dists’
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‘dists’
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Documented arguments not in \usage in Rd file 'aux_mat.Rd':
‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’
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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.
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- 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 ... [35s/45s] 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
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- DONE
Status: 2 ERRORs, 4 NOTEs