• using R Under development (unstable) (2024-12-21 r87453 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.3.0     GNU Fortran (GCC) 13.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'MarZIC/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'MarZIC' version '1.0.0'
• package encoding: UTF-8
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• checking package dependencies ... OK
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• checking whether package 'MarZIC' can be installed ... OK See the install log for details.
• used C++ compiler: 'g++.exe (GCC) 13.3.0'
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [3s] ERROR Running examples in 'MarZIC-Ex.R' failed The error most likely occurred in: > ### Name: MarZIC > ### Title: Marginal Mediation Model for Zero-Inflated Compositional > ### Mediators > ### Aliases: MarZIC > > ### ** Examples > > { + library(MarZIC) + + ## A make up example with 2 taxon and 20 subjects. + set.seed(1) + nSub <- 20 + nTaxa <- 2 + ## generate covariate of interest X + X <- rbinom(nSub, 1, 0.5) + ## generate confounders + conf1<-rnorm(nSub) + conf2<-rbinom(nSub,1,0.5) + ## generate mean of each taxon. All taxon are having the same mean for simplicity. + mu <- exp(-5 + X + 0.1 * conf1 + 0.1 * conf2) / + (1 + exp(-5 + X + 0.1 * conf1 + 0.1 * conf2)) + phi <- 10 + + ## generate true RA + M_taxon<-t(sapply(mu,function(x) dirmult::rdirichlet(n=1,rep(x*phi,nTaxa)))) + + P_zero <- exp(-3 + 0.3 * X + 0.1 * conf1 + 0.1 * conf2) / + (1 + exp(-3 + 0.3 * X + 0.1 * conf1 + 0.1 * conf2)) + + non_zero_ind <- t(sapply(P_zero,function(x) 1-rbinom(nTaxa,1,rep(x,nTaxa)))) + + True_RA<-t(apply(M_taxon*non_zero_ind,1,function(x) x/sum(x))) + + ## generate outcome Y based on true RA + Y <- 1 + 100 * True_RA[,1] + 5 * (True_RA[,1] > 0) + X + conf1 + conf2 + rnorm(nSub) + + ## library size was set to 10,000 for all subjects for simplicity. + libsize <- 10000 + + ## generate observed RA + observed_AA <- floor(M_taxon*libsize*non_zero_ind) + + observed_RA <- t(apply(observed_AA,1,function(x) x/sum(x))) + colnames(observed_RA)<-paste0("rawCount",seq_len(nTaxa)) + CovData <- cbind(Y = Y, X = X, libsize = libsize, conf1 = conf1, conf2 = conf2) + + + ## run the analysis + res <- MarZIC( + MicrobData = observed_RA, + CovData = CovData, + lib_name = "libsize", + y_name = "Y", + x_name = "X", + conf_name = c("conf1","conf2"), + taxa_of_interest = NULL, + num_cores = 1, + mediator_mix_range = 1 + ) + } One or more reads are missing. Subjects with missing were removed from analysis Error in unserialize(socklist[[n]]) : error reading from connection Calls: MarZIC Execution halted Error in serialize(data, node$con) : error writing to connection Calls: <Anonymous> ... postNode -> sendData -> sendData.SOCKnode -> serialize
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s] ERROR Error(s) in re-building vignettes: --- re-building 'MarZIC.Rmd' using rmarkdown Quitting from lines 113-127 [unnamed-chunk-3] (MarZIC.Rmd) Error: processing vignette 'MarZIC.Rmd' failed with diagnostics: error reading from connection --- failed re-building 'MarZIC.Rmd' SUMMARY: processing the following file failed:   'MarZIC.Rmd' Error: Vignette re-building failed. Execution halted Error in serialize(data, node$con) : error writing to connection Calls: <Anonymous> ... postNode -> sendData -> sendData.SOCKnode -> serialize
• checking PDF version of manual ... [21s] OK
• checking HTML version of manual ... [1s] OK
• DONE

Status: 2 ERRORs