* using log directory ‘/srv/hornik/tmp/CRAN_pretest/jointest.Rcheck’ * using R Under development (unstable) (2024-12-10 r87437) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘jointest/DESCRIPTION’ ... OK * this is package ‘jointest’ version ‘2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Livio Finos ’ New submission Possibly misspelled words in DESCRIPTION: Familywise (9:181) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Remotes’ The Title field should be in title case. Current version is: ‘Multivariate testing through joint resampling-based tests’ In title case that is: ‘Multivariate Testing Through Joint Resampling-Based Tests’ The Description field contains ) to allow for multivariate testing, i.e., Please write DOIs as . * 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 ‘jointest’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... 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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 ... [0s/0s] 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 ... [5s/5s] ERROR Running examples in ‘jointest-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: join_flipscores > ### Title: join tests from multiverse models > ### Aliases: join_flipscores > > ### ** Examples > > library(jointest) > set.seed(123) > > > #EXAMPLE 1: Simulate data: > n=20 > D=data.frame(X=rnorm(n),Z1=rnorm(n),Z2=rnorm(n)) > D$Y=D$Z1+D$X+rnorm(n) > > # Run four glms abd combine it in a list > mod1=glm(Y~X+Z1+Z2,data=D) > mod2=glm(Y~X+poly(Z1,2)+Z2,data=D) > mod3=glm(Y~X+poly(Z1,2)+poly(Z2,2),data=D) > mod4=glm(Y~X+Z1+poly(Z2,2),data=D) > mods=list(mod1=mod1,mod2=mod2,mod3=mod3,mod4=mod4) > > # flipscores jointly on all models > res=join_flipscores(mods,n_flips = 1000) > summary(combine(res)) Model Coeff Stat nTests S p 1 Overall many maxT 20 19.78375 0.012 > summary(combine(res, by="Model")) Model Coeff Stat nTests S p 1 mod1 many maxT 4 19.78375 0.012 2 mod2 many maxT 5 15.38036 0.023 3 mod3 many maxT 6 14.31866 0.022 4 mod4 many maxT 5 17.62979 0.010 > summary(combine_contrasts(res)) Model Coeff Stat nTests S p 1 mod1 (Intercept) Mahalanobis 1 0.015397573 0.645 2 mod1 X Mahalanobis 1 0.063345731 0.012 3 mod1 Z1 Mahalanobis 1 0.081964684 0.001 4 mod1 Z2 Mahalanobis 1 0.028061470 0.396 5 mod2 (Intercept) Mahalanobis 1 0.028543183 0.373 6 mod2 X Mahalanobis 1 0.063464285 0.023 7 mod2 poly(Z1, 2) Mahalanobis 2 6.785258498 0.007 8 mod2 Z2 Mahalanobis 1 0.005339577 0.881 9 mod3 (Intercept) Mahalanobis 1 0.029423638 0.374 10 mod3 X Mahalanobis 1 0.065802300 0.022 11 mod3 poly(Z1, 2) Mahalanobis 2 6.106607329 0.010 12 mod3 poly(Z2, 2) Mahalanobis 2 0.957008442 0.647 13 mod4 (Intercept) Mahalanobis 1 0.018831666 0.565 14 mod4 X Mahalanobis 1 0.066979615 0.010 15 mod4 Z1 Mahalanobis 1 0.082481423 0.001 16 mod4 poly(Z2, 2) Mahalanobis 2 1.171827830 0.585 > > #Simulate multivariate (50) bionomial responses > set.seed(123) > n=30 > D=data.frame(X=rnorm(n),Z=rnorm(n)) > Y=replicate(50,rbinom(n,1,plogis(.5*D$Z+.5*D$X))) > colnames(Y)=paste0("Y",1:50) > D=cbind(D,Y) > mods=lapply(1:50,function(i)eval(parse(text= + paste(c("glm(formula(Y",i,"~X+Z),data=D,family='binomial')"),collapse="")))) > # flipscores jointly on all models > res=join_flipscores(mods,n_flips = 1000,tested_coeffs ="X") Warning in names(model$call$data)[1] <- yname : number of items to replace is not a multiple of replacement length Warning in formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. Warning in formula.character(object, env = baseenv()) : Using formula(x) is deprecated when x is a character vector of length > 1. Consider formula(paste(x, collapse = " ")) instead. Error in eval(family$initialize) : for the 'binomial' family, y must be a vector of 0 and 1's or a 2 column matrix where col 1 is no. successes and col 2 is no. failures Calls: join_flipscores ... eval -> glm -> eval -> eval -> glm.fit -> eval -> eval Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [6s/6s] OK * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE