• using R Under development (unstable) (2026-09-07 r90508)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.1     flang version 23.1.1
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-08 15:04:27 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘MultiPhen/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MultiPhen’ version ‘2.0.4’
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• checking examples ... ERROR Running examples in ‘MultiPhen-Ex.R’ failed The error most likely occurred in: > ### Name: mPhen > ### Title: A function for the genetic association testing of multiple > ### phenotypes > ### Aliases: mPhen > ### Keywords: genetics GWAS regression multiple phenotypes association > > ### ** Examples > > data(snps); data(snps.imputed); data(pheno) > opts = mPhen.options(c("regression","pheno.input")) > res = mPhen(snps, pheno, phenotypes = "all", + covariates = c('testPheno3', 'testPheno4'),opts = opts) [1] "excluding 0 samples based on exclusion criteria" > # performs a MultiPhen analysis, with snp as outcome, > # and phenotypes testPheno1, testPheno2 as predictors, > #with testPheno3 and testPheno4 as covariates using ordinal regression > > res = mPhen(snps, pheno, phenotypes = c('testPheno1', 'testPheno2'), + covariates = c('testPheno3', 'testPheno4'), resids = 'testPheno5', opts = opts) [1] "excluding 0 samples based on exclusion criteria" > # the same as above, with the fifth phenotype as residual > > res = mPhen(snps[,2, drop = FALSE], pheno, phenotypes = c('testPheno1', 'testPheno2'), + covariates = 'testPheno3', opts = opts) [1] "excluding 0 samples based on exclusion criteria" > # please note the use use of drop = FALSE if analysing only one SNP > > > res = mPhen(snps.imputed, pheno, phenotypes = c('testPheno1', 'testPheno2'), + covariates = 'testPheno3', opts = opts) [1] "excluding 0 samples based on exclusion criteria" Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred NULL [1] "polr failed, using Gaussian" Error in eval(mf, parent.frame()) : object 'string' not found Calls: mPhen ... <Anonymous> -> model.frame.default -> is.data.frame Execution halted
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• DONE

Status: 1 ERROR