• using R Under development (unstable) (2025-02-19 r87756)
• 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 ... [62s/160s] OK See the install log 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 ... [6s/16s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/13s] OK
• checking whether the package can be unloaded cleanly ... [5s/13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/13s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/13s] OK
• checking loading without being on the library search path ... [5s/13s] OK
• checking whether startup messages can be suppressed ... [6s/14s] 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 ... [155s/403s] 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 ... [32m/26m] 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 ... [145s/217s] OK   Running ‘testthat.R’ [144s/217s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [36m/46m] 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/19s] OK
• checking HTML version of manual ... [9s/16s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs