* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/spmodel.Rcheck’
* using R Under development (unstable) (2025-02-23 r87798)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘spmodel/DESCRIPTION’ ... OK
* this is package ‘spmodel’ version ‘0.9.0’
* 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 ‘spmodel’ can be installed ... [60s/88s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/spmodel-00install.html' for details.
* 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 whether startup messages can be suppressed ... 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 ... [147s/194s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31m/24m] ERROR
Running examples in ‘spmodel-Ex.R’ failed
The error most likely occurred in:
> ### Name: augment.spmodel
> ### Title: Augment data with information from fitted model objects
> ### Aliases: augment.spmodel augment.splm augment.spautor augment.spglm
> ### augment.spgautor
>
> ### ** Examples
>
> spmod <- splm(z ~ water + tarp,
+ data = caribou,
+ spcov_type = "exponential", xcoord = x, ycoord = y
+ )
> augment(spmod)
# A tibble: 30 × 10
z water tarp x y .fitted .resid .hat .cooksd .std.resid
<dbl> <fct> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 2.42 Y clear 1 6 1.97 0.454 0.116 0.209 2.53
2 2.44 Y shade 2 6 2.25 0.190 0.137 0.0468 1.09
3 1.81 Y none 3 6 2.05 -0.237 0.137 0.0752 -1.38
4 1.97 N clear 4 6 2.05 -0.0838 0.174 0.00211 -0.200
5 2.38 N shade 5 6 2.34 0.0407 0.153 0.0159 0.594
6 2.22 Y none 1 5 2.05 0.177 0.147 0.0434 1.00
7 2.10 N clear 2 5 2.05 0.0512 0.156 0.00936 0.450
8 1.80 Y clear 3 5 1.97 -0.163 0.122 0.0135 -0.624
9 1.96 Y shade 4 5 2.25 -0.290 0.119 0.0642 -1.38
10 2.10 Y none 5 5 2.05 0.0522 0.131 0.0264 0.837
# ℹ 20 more rows
> spmod_sulf <- splm(sulfate ~ 1, data = sulfate, spcov_type = "exponential")
> augment(spmod_sulf)
Simple feature collection with 197 features and 6 fields
Geometry type: POINT
Dimension: XY
Bounding box: xmin: -2292550 ymin: 386181.1 xmax: 2173345 ymax: 3090370
Projected CRS: NAD83 / Conus Albers
# A tibble: 197 × 7
sulfate .fitted .resid .hat .cooksd .std.resid geometry
* <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <POINT [m]>
1 12.9 5.92 7.00 0.00334 0.00161 -0.694 (817738.8 1080571)
2 20.2 5.92 14.2 0.00256 0.00192 0.865 (914593.6 1295545)
3 16.8 5.92 10.9 0.00259 0.000395 0.390 (359574.1 1178228)
4 16.2 5.92 10.3 0.00239 0.000363 0.390 (265331.9 1239089)
5 7.86 5.92 1.93 0.00202 0.00871 -2.07 (304528.8 1453636)
6 15.4 5.92 9.43 0.00201 0.000240 0.345 (162932.8 1451625)
7 0.986 5.92 -4.94 0.00380 0.000966 -0.503 (-1437776 1568022)
8 0.425 5.92 -5.50 0.0138 0.00584 -0.646 (-1572878 1125529)
9 3.58 5.92 -2.34 0.00673 0.0000148 -0.0467 (-1282009 1204889)
10 2.38 5.92 -3.54 0.0123 0.0000139 -0.0335 (-1972775 1464991)
# ℹ 187 more rows
> augment(spmod_sulf, newdata = sulfate_preds)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [138s/164s] OK
Running ‘testthat.R’ [138s/164s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31m/19m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/spmodel.Rcheck/vign_test/spmodel/vignettes/introduction_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 88879 bytes
Input file size = 89077 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 75790
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 = 75790
Output IDAT size = 75790 bytes (13089 bytes decrease)
Output file size = 75868 bytes (13209 bytes = 14.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spmodel.Rcheck/vign_test/spmodel/vignettes/introduction_files/figure-html/unnamed-chunk-14-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 130624 bytes
Input file size = 130882 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 100995
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 = 100995
Output IDAT size = 100995 bytes (29629 bytes decrease)
Output file size = 101073 bytes (29809 bytes = 22.78% decrease)
* checking PDF version of manual ... [13s/14s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs