• using R Under development (unstable) (2026-11-08 r90859)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 23.1.5 (2)     Debian flang version 23.1.5 (2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-11-10 02:56:44 UTC
• checking for file ‘gdm/DESCRIPTION’ ... OK
• this is package ‘gdm’ version ‘1.6.0-7’
• package encoding: UTF-8
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• checking package dependencies ... INFO Package suggested but not available for checking: 'terra'
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• checking whether package ‘gdm’ can be installed ... OK See the install log for details.
• used C compiler: ‘Debian clang version 23.1.5 (2)’
• used C++ compiler: ‘Debian clang version 23.1.5 (2)’
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• checking examples ... [7s/10s] ERROR Running examples in ‘gdm-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gdm > ### Title: Fit a Generalized Dissimilarity Model to Tabular Site-Pair Data > ### Aliases: gdm > ### Keywords: gdm > > ### ** Examples > > ##fit table environmental data > # format site-pair table using the southwest data table > head(southwest)   species site awcA phTotal sandA shcA solumDepth bio5 bio6 1 spp1 1066 14.4725 546.1800 71.3250 178.8650 875.1725 31.43824 5.058823 2 spp1 1026 16.2575 470.9950 68.8975 105.8400 928.4925 33.14412 4.852941 3 spp1 1025 23.1375 459.7425 71.4700 88.3550 892.2275 32.84000 4.817143 4 spp1 1026 16.2575 470.9950 68.8975 105.8400 928.4925 33.14412 4.852941 5 spp1 1027 17.0175 489.3950 74.6775 147.2125 951.9050 33.17813 4.590625 6 spp1 1047 17.3625 515.0825 75.7525 164.1875 981.4750 32.61579 4.676316      bio15 bio18 bio19 Lat Long 1 40.38235 0 132.6471 -32.99425 118.7573 2 48.20588 0 140.2941 -32.04285 118.3495 3 53.88571 43 145.0571 -31.99067 117.8260 4 48.20588 0 140.2941 -32.04285 118.3495 5 44.00000 0 135.6875 -32.09326 118.8736 6 42.00000 0 134.0263 -32.54354 118.8157 > sppData <- southwest[, c(1,2,13,14)] > envTab <- southwest[, c(2:ncol(southwest))] > > sitePairTab <- formatsitepair(sppData, 2, XColumn="Long", YColumn="Lat", sppColumn="species", + siteColumn="site", predData=envTab) Warning in formatsitepair(sppData, 2, XColumn = "Long", YColumn = "Lat", :   No abundance column was specified, so the biological data are assumed to be presences. Aggregation function missing: defaulting to length > > ##fit table GDM > gdmTabMod <- gdm(sitePairTab, geo=TRUE) > summary(gdmTabMod) [1] [1] [1] GDM Modelling Summary [1] Creation Date: Tue Nov 10 03:58:40 2026 [1] [1] Name: gdmTabMod [1] [1] Data: sitePairTab [1] [1] Samples: 4371 [1] [1] Geographical distance used in model fitting? TRUE [1] [1] NULL Deviance: 651.914 [1] GDM Deviance: 129.025 [1] Percent Deviance Explained: 80.208 [1] [1] Intercept: 0.277 [1] [1] PREDICTOR ORDER BY SUM OF I-SPLINE COEFFICIENTS: [1] [1] Predictor 1: bio19 [1] Splines: 3 [1] Min Knot: 114.394 [1] 50% Knot: 172.416 [1] Max Knot: 554.771 [1] Coefficient[1]: 0.941 [1] Coefficient[2]: 0.868 [1] Coefficient[3]: 0 [1] Sum of coefficients for bio19: 1.809 [1] [1] Predictor 2: phTotal [1] Splines: 3 [1] Min Knot: 277.978 [1] 50% Knot: 584.609 [1] Max Knot: 1860.37 [1] Coefficient[1]: 1.127 [1] Coefficient[2]: 0.23 [1] Coefficient[3]: 0 [1] Sum of coefficients for phTotal: 1.357 [1] [1] Predictor 3: bio5 [1] Splines: 3 [1] Min Knot: 25.571 [1] 50% Knot: 32.16 [1] Max Knot: 36.188 [1] Coefficient[1]: 0.127 [1] Coefficient[2]: 0.453 [1] Coefficient[3]: 0.114 [1] Sum of coefficients for bio5: 0.694 [1] [1] Predictor 4: solumDepth [1] Splines: 3 [1] Min Knot: 705.02 [1] 50% Knot: 1017.628 [1] Max Knot: 1247.705 [1] Coefficient[1]: 0.682 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0 [1] Sum of coefficients for solumDepth: 0.682 [1] [1] Predictor 5: awcA [1] Splines: 3 [1] Min Knot: 12.975 [1] 50% Knot: 22.186 [1] Max Knot: 50.7 [1] Coefficient[1]: 0 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0.523 [1] Sum of coefficients for awcA: 0.523 [1] [1] Predictor 6: Geographic [1] Splines: 3 [1] Min Knot: 0.452 [1] 50% Knot: 2.46 [1] Max Knot: 6.532 [1] Coefficient[1]: 0.014 [1] Coefficient[2]: 0.372 [1] Coefficient[3]: 0 [1] Sum of coefficients for Geographic: 0.386 [1] [1] Predictor 7: sandA [1] Splines: 3 [1] Min Knot: 56.697 [1] 50% Knot: 72.951 [1] Max Knot: 83.993 [1] Coefficient[1]: 0.092 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0.139 [1] Sum of coefficients for sandA: 0.231 [1] [1] Predictor 8: shcA [1] Splines: 3 [1] Min Knot: 78.762 [1] 50% Knot: 179.351 [1] Max Knot: 521.985 [1] Coefficient[1]: 0 [1] Coefficient[2]: 0.156 [1] Coefficient[3]: 0 [1] Sum of coefficients for shcA: 0.156 [1] [1] Predictor 9: bio6 [1] Splines: 3 [1] Min Knot: 4.373 [1] 50% Knot: 5.509 [1] Max Knot: 9.224 [1] Coefficient[1]: 0.121 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0 [1] Sum of coefficients for bio6: 0.121 [1] [1] Predictor 10: bio15 [1] Splines: 3 [1] Min Knot: 29.167 [1] 50% Knot: 55.008 [1] Max Knot: 87.143 [1] Coefficient[1]: 0.027 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0 [1] Sum of coefficients for bio15: 0.027 [1] [1] Predictor 11: bio18 [1] Splines: 3 [1] Min Knot: 0 [1] 50% Knot: 0 [1] Max Knot: 52 [1] Coefficient[1]: 0 [1] Coefficient[2]: 0 [1] Coefficient[3]: 0 [1] Sum of coefficients for bio18: 0 > > ##fit raster environmental data > ##sets up site-pair table > rastFile <- system.file("./extdata/swBioclims.grd", package="gdm") > envRast <- terra::rast(rastFile) Error in loadNamespace(x) : there is no package called ‘terra’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR