CRAN Package Check Results for Package forestPSD

Last updated on 2025-09-12 01:52:38 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.0.0	1.46	23.01	24.47	OK
r-devel-linux-x86_64-debian-gcc	1.0.0	1.62	19.63	21.25	ERROR
r-devel-linux-x86_64-fedora-clang	1.0.0			38.47	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.0			36.28	ERROR
r-devel-windows-x86_64	1.0.0	3.00	43.00	46.00	OK
r-patched-linux-x86_64	1.0.0	2.05	22.30	24.35	OK
r-release-linux-x86_64	1.0.0	1.56	21.97	23.53	OK
r-release-macos-arm64	1.0.0			32.00	OK
r-release-macos-x86_64	1.0.0			27.00	OK
r-release-windows-x86_64	1.0.0	3.00	43.00	46.00	OK
r-oldrel-macos-arm64	1.0.0			18.00	OK
r-oldrel-macos-x86_64	1.0.0			26.00	OK
r-oldrel-windows-x86_64	1.0.0	4.00	48.00	52.00	OK

Check Details

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘forestPSD-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: psdfun > ### Title: Regression analysis for survival curves. > ### Aliases: psdfun > > ### ** Examples > > data(Npop) > psd_D1<-psdfun(ax=Npop$ax,index="Deevey1") > psd_D1 $Summary Formula: ax ~ a + b * age Parameters: Estimate Std. Error t value Pr(>|t|) a 5603.9 1062.0 5.277 0.000509 *** b -642.3 156.6 -4.102 0.002669 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 1642 on 9 degrees of freedom Number of iterations to convergence: 2 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 2206682 1485.49 0.6515192 0.564399 1234.35 17.69146 0.7053431 197.8937 BIC 1 197.8937 $Data age ageclass ax predict 1 1 I 8283 4961.5455 2 2 II 5238 4319.2364 3 3 III 1921 3676.9273 4 4 IV 1425 3034.6182 5 5 V 926 2392.3091 6 6 VI 659 1750.0000 7 7 VII 479 1107.6909 8 8 VIII 228 465.3818 9 9 IX 57 -176.9273 10 10 X 24 -819.2364 11 11 XI 10 -1461.5455 > psd_D2<-psdfun(ax=Npop$ax,index="Deevey2") > psd_D2 $Summary Formula: ax ~ a * exp(-b * age) Parameters: Estimate Std. Error t value Pr(>|t|) a 1.504e+04 9.717e+02 15.48 8.59e-08 *** b 5.828e-01 3.883e-02 15.01 1.12e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 318.7 on 9 degrees of freedom Number of iterations to convergence: 17 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 83111.3 288.2903 0.9869709 0.9837137 188.8823 0.4079135 0.1079327 161.8239 BIC 1 161.8239 $Data age ageclass ax predict 1 1 I 8283 8396.40389 2 2 II 5238 4687.87598 3 3 III 1921 2617.33255 4 4 IV 1425 1461.30779 5 5 V 926 815.87663 6 6 VI 659 455.51983 7 7 VII 479 254.32560 8 8 VIII 228 141.99494 9 9 IX 57 79.27854 10 10 X 24 44.26276 11 11 XI 10 24.71276 > psd_D3<-psdfun(ax=Npop$ax,index="Deevey3") > psd_D3 $Summary Formula: ax ~ a * (age^-b) Parameters: Estimate Std. Error t value Pr(>|t|) a 8691.1232 633.3189 13.723 2.44e-07 *** b 1.2598 0.1326 9.499 5.48e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 649 on 9 degrees of freedom Number of iterations to convergence: 18 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 344662.5 587.0797 0.9491095 0.9363869 442.1638 6.578955 0.252665 177.4702 BIC 1 177.4702 $Data age ageclass ax predict 1 1 I 8283 8691.1232 2 2 II 5238 3629.4310 3 3 III 1921 2177.7043 4 4 IV 1425 1515.6579 5 5 V 926 1144.2318 6 6 VI 659 909.4138 7 7 VII 479 748.8969 8 8 VIII 228 632.9419 9 9 IX 57 545.6597 10 10 X 24 477.8336 11 11 XI 10 423.7700 > library(ggplot2) > psdnls.p<-ggplot()+geom_bar(aes(x=age,y=ax,group=ageclass),data=psd_D2$Data,stat = "identity")+ + geom_line(aes(x=age,y=predict),color="blue",linewidth=1,data=psd_D2$Data)+ + geom_text(aes(x=10,y=7700),label=expression(paste(italic(y),"=aexp(-b",italic(x),")")))+ + geom_text(aes(x=10,y=7300),label=expression(paste(R^2,"=0.987")))+ + scale_x_continuous(breaks=1:11)+ + scale_x_discrete(limits=psd_D2$Data$ageclass)+ + xlab("Age class")+ylab("Number of individuals") Scale for x is already present. Adding another scale for x, which will replace the existing scale. > psdnls.p Error in `geom_text()`: ! Problem while setting up geom aesthetics. ℹ Error occurred in the 3rd layer. Caused by error in `list_sizes()`: ! `x$label` must be a vector, not an expression vector. Backtrace: ▆ 1. ├─base (local) `<fn>`(x) 2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x) 3. │ ├─ggplot2::ggplot_build(x) 4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$compute_geom_2(d, theme = plot@theme) 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) 15. │ └─self$geom$use_defaults(...) 16. │ └─ggplot2 (local) use_defaults(..., self = self) 17. │ └─ggplot2:::check_aesthetics(new_params, nrow(data)) 18. │ └─vctrs::list_sizes(x) 19. └─vctrs:::stop_scalar_type(`<fn>`(`<expression>`), "x$label", `<env>`) 20. └─vctrs:::stop_vctrs(...) 21. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.0
Check: dependencies in R code
Result: NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘reshape2’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘forestPSD-Ex.R’ failed The error most likely occurred in: > ### Name: psdfun > ### Title: Regression analysis for survival curves. > ### Aliases: psdfun > > ### ** Examples > > data(Npop) > psd_D1<-psdfun(ax=Npop$ax,index="Deevey1") > psd_D1 $Summary Formula: ax ~ a + b * age Parameters: Estimate Std. Error t value Pr(>|t|) a 5603.9 1062.0 5.277 0.000509 *** b -642.3 156.6 -4.102 0.002669 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 1642 on 9 degrees of freedom Number of iterations to convergence: 2 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 2206682 1485.49 0.6515192 0.564399 1234.35 17.69146 0.7053431 197.8937 BIC 1 197.8937 $Data age ageclass ax predict 1 1 I 8283 4961.5455 2 2 II 5238 4319.2364 3 3 III 1921 3676.9273 4 4 IV 1425 3034.6182 5 5 V 926 2392.3091 6 6 VI 659 1750.0000 7 7 VII 479 1107.6909 8 8 VIII 228 465.3818 9 9 IX 57 -176.9273 10 10 X 24 -819.2364 11 11 XI 10 -1461.5455 > psd_D2<-psdfun(ax=Npop$ax,index="Deevey2") > psd_D2 $Summary Formula: ax ~ a * exp(-b * age) Parameters: Estimate Std. Error t value Pr(>|t|) a 1.504e+04 9.717e+02 15.48 8.59e-08 *** b 5.828e-01 3.883e-02 15.01 1.12e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 318.7 on 9 degrees of freedom Number of iterations to convergence: 17 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 83111.3 288.2903 0.9869709 0.9837137 188.8823 0.4079135 0.1079327 161.8239 BIC 1 161.8239 $Data age ageclass ax predict 1 1 I 8283 8396.40389 2 2 II 5238 4687.87598 3 3 III 1921 2617.33255 4 4 IV 1425 1461.30779 5 5 V 926 815.87663 6 6 VI 659 455.51983 7 7 VII 479 254.32560 8 8 VIII 228 141.99494 9 9 IX 57 79.27854 10 10 X 24 44.26276 11 11 XI 10 24.71276 > psd_D3<-psdfun(ax=Npop$ax,index="Deevey3") > psd_D3 $Summary Formula: ax ~ a * (age^-b) Parameters: Estimate Std. Error t value Pr(>|t|) a 8691.1232 633.3189 13.723 2.44e-07 *** b 1.2598 0.1326 9.499 5.48e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 649 on 9 degrees of freedom Number of iterations to convergence: 18 Achieved convergence tolerance: 1.49e-08 $Goodness MSE RMSE Rsquare adj.Rsquare MAE MAPE RASE AIC 1 344662.5 587.0797 0.9491095 0.9363869 442.1638 6.578955 0.252665 177.4702 BIC 1 177.4702 $Data age ageclass ax predict 1 1 I 8283 8691.1232 2 2 II 5238 3629.4310 3 3 III 1921 2177.7043 4 4 IV 1425 1515.6579 5 5 V 926 1144.2318 6 6 VI 659 909.4138 7 7 VII 479 748.8969 8 8 VIII 228 632.9419 9 9 IX 57 545.6597 10 10 X 24 477.8336 11 11 XI 10 423.7700 > library(ggplot2) > psdnls.p<-ggplot()+geom_bar(aes(x=age,y=ax,group=ageclass),data=psd_D2$Data,stat = "identity")+ + geom_line(aes(x=age,y=predict),color="blue",linewidth=1,data=psd_D2$Data)+ + geom_text(aes(x=10,y=7700),label=expression(paste(italic(y),"=aexp(-b",italic(x),")")))+ + geom_text(aes(x=10,y=7300),label=expression(paste(R^2,"=0.987")))+ + scale_x_continuous(breaks=1:11)+ + scale_x_discrete(limits=psd_D2$Data$ageclass)+ + xlab("Age class")+ylab("Number of individuals") Scale for x is already present. Adding another scale for x, which will replace the existing scale. > psdnls.p Error in `geom_text()`: ! Problem while setting up geom aesthetics. ℹ Error occurred in the 3rd layer. Caused by error in `list_sizes()`: ! `x$label` must be a vector, not an expression vector. Backtrace: ▆ 1. ├─base (local) `<fn>`(x) 2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x) 3. │ ├─ggplot2::ggplot_build(x) 4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$compute_geom_2(d, theme = plot@theme) 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) 15. │ └─self$geom$use_defaults(...) 16. │ └─ggplot2 (local) use_defaults(..., self = self) 17. │ └─ggplot2:::check_aesthetics(new_params, nrow(data)) 18. │ └─vctrs::list_sizes(x) 19. └─vctrs:::stop_scalar_type(`<fn>`(`<expression>`), "x$label", `<env>`) 20. └─vctrs:::stop_vctrs(...) 21. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc