Last updated on 2024-04-09 08:54:53 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4.1 | 62.09 | 131.05 | 193.14 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4.1 | 42.08 | 95.06 | 137.14 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4.1 | 247.40 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4.1 | 252.80 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.4.1 | 51.00 | 132.00 | 183.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.4.1 | 61.45 | 120.05 | 181.50 | ERROR | |
| r-release-linux-x86_64 | 1.0.4.1 | 54.82 | 124.34 | 179.16 | ERROR | |
| r-release-macos-arm64 | 1.0.4.1 | 89.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.4.1 | 143.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.4.1 | 62.00 | 159.00 | 221.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.4.1 | 74.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.0.4.1 | 61.00 | 150.00 | 211.00 | ERROR |
Version: 1.0.4.1
Check: C++ specification
Result: NOTE
Specified C++11: please drop specification unless essential
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.0.4.1
Check: Rd files
Result: 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
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64
Version: 1.0.4.1
Check: Rd \usage sections
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64
Version: 1.0.4.1
Check: examples
Result: ERROR
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.4.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.4.1
Check: re-building of vignette outputs
Result: 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
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smile.Rcheck/vign_test/smile/vignettes/sai_files/figure-html/ggplot-obs-est-viz-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23178 bytes
Input file size = 23280 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19948
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19948
Output IDAT size = 19948 bytes (3230 bytes decrease)
Output file size = 20026 bytes (3254 bytes = 13.98% decrease)
--- finished re-building ‘sai.Rmd’
--- re-building ‘sf-to-spm.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smile.Rcheck/vign_test/smile/vignettes/sf-to-spm_files/figure-html/read-data-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 33382 bytes
Input file size = 33508 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24452
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24452
Output IDAT size = 24452 bytes (8930 bytes decrease)
Output file size = 24530 bytes (8978 bytes = 26.79% decrease)
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.4.1
Check: installed package size
Result: NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 1.0.4.1
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.4.1
Check: re-building of vignette outputs
Result: 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
** Processing: /data/gannet/ripley/R/packages/tests-clang/smile.Rcheck/vign_test/smile/vignettes/sai_files/figure-html/ggplot-obs-est-viz-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23167 bytes
Input file size = 23269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19953
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19953
Output IDAT size = 19953 bytes (3214 bytes decrease)
Output file size = 20031 bytes (3238 bytes = 13.92% decrease)
--- finished re-building ‘sai.Rmd’
--- re-building ‘sf-to-spm.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/smile.Rcheck/vign_test/smile/vignettes/sf-to-spm_files/figure-html/read-data-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 33744 bytes
Input file size = 33870 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24717
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24717
Output IDAT size = 24717 bytes (9027 bytes decrease)
Output file size = 24795 bytes (9075 bytes = 26.79% decrease)
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.4.1
Check: re-building of vignette outputs
Result: 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
** Processing: /data/gannet/ripley/R/packages/tests-devel/smile.Rcheck/vign_test/smile/vignettes/sai_files/figure-html/ggplot-obs-est-viz-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23167 bytes
Input file size = 23269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19953
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19953
Output IDAT size = 19953 bytes (3214 bytes decrease)
Output file size = 20031 bytes (3238 bytes = 13.92% decrease)
--- finished re-building ‘sai.Rmd’
--- re-building ‘sf-to-spm.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/smile.Rcheck/vign_test/smile/vignettes/sf-to-spm_files/figure-html/read-data-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 33744 bytes
Input file size = 33870 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24717
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24717
Output IDAT size = 24717 bytes (9027 bytes decrease)
Output file size = 24795 bytes (9075 bytes = 26.79% decrease)
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.4.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64