• using R Under development (unstable) (2025-09-03 r88788)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b2)     Debian flang-new version 19.1.7 (3+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
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• this is package ‘agriTutorial’ version ‘0.1.5’
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• checking CRAN incoming feasibility ... [0s/1s] NOTE Maintainer: ‘Rodney Edmondson <rodney.edmondson@gmail.com>’ Found the following URLs which should use \doi (with the DOI name only):   File ‘agriTutorial.Rd’:     http://dx.doi.org/10.1111/jac.12267   File ‘example1.Rd’:     http://dx.doi.org/10.1111/jac.12267   File ‘example2.Rd’:     http://dx.doi.org/10.1111/jac.12267   File ‘example3.Rd’:     http://dx.doi.org/10.1111/jac.12267   File ‘example4.Rd’:     http://dx.doi.org/10.1111/jac.12267   File ‘example5.Rd’:     http://dx.doi.org/10.1111/jac.12267
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• checking examples ... [6s/8s] ERROR Running examples in ‘agriTutorial-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: example4 > ### Title: Example 4: One qualitative treatment factor with repeated > ### measurements over time. > ### Aliases: example4 > > ### ** Examples > > > ## ************************************************************************************* > ## How to run the code > ## ************************************************************************************* > > ## Either type example("example4") to run ALL the examples succesively > ## or copy and paste examples sucessively, as required > > ## ************************************************************************************* > ## Options and required packages > ## ************************************************************************************* > > options(contrasts = c('contr.treatment','contr.poly')) > require(nlme) Loading required package: nlme > > ## ************************************************************************************* > ## Section 1: Polynomials for weeks and blocks contrasts > ## ************************************************************************************* > > sorghum$rawWeeks = poly(sorghum$varweek, degree = 4, raw = TRUE) > sorghum$polWeeks = poly(sorghum$varweek, degree = 4, raw = FALSE) > sorghum$polBlocks = poly(sorghum$varblock, degree = 4, raw = FALSE) > sorghum$factblock = factor(sorghum$varblock) > > ## ************************************************************************************* > ## Section 2: Various correlation models assuming full factorial blocks and weeks model > ## ************************************************************************************* > > AIC = NULL > logLik = NULL > Model = c("ID", "CS", "AR(1)", "AR(1) + nugget", "UN") > > ## independent uncorrelated random plots > full_indy = gls(y ~ factweek * (Replicate + variety), sorghum) > anova(full_indy) Denom. DF: 60                    numDF F-value p-value (Intercept) 1 80947.08 <.0001 factweek 4 220.90 <.0001 Replicate 4 358.86 <.0001 variety 3 334.87 <.0001 factweek:Replicate 16 1.82 0.0495 factweek:variety 12 4.48 <.0001 > AIC = c(AIC, AIC(full_indy)) Error in ll(object) : could not find function "ll" Calls: AIC -> AIC.default Execution halted
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Status: 1 ERROR, 1 NOTE