* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/eclust.Rcheck’ * using R Under development (unstable) (2024-05-11 r86532) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.1.0 GNU Fortran (GCC) 14.1.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘eclust/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘eclust’ version ‘0.1.0’ * package encoding: UTF-8 * 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 ‘eclust’ can be installed ... [10s/40s] OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘pander’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s/56s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... 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 ... 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 ... [19s/82s] ERROR Running examples in ‘eclust-Ex.R’ failed The error most likely occurred in: > ### Name: s_generate_data_mars > ### Title: Generate non linear response and test and training sets for > ### non-linear simulation study > ### Aliases: s_generate_data_mars > > ### ** Examples > > library(magrittr) > > # simulation parameters > rho = 0.90; p = 500 ;SNR = 1 ; n = 200; n0 = n1 = 100 ; nActive = p*0.10 ; cluster_distance = "tom"; > Ecluster_distance = "difftom"; rhoOther = 0.6; betaMean = 2; > alphaMean = 1; betaE = 3; distanceMethod = "euclidean"; clustMethod = "hclust"; > cutMethod = "dynamic"; agglomerationMethod = "average" > > #in this simulation its blocks 3 and 4 that are important > #leaveOut: optional specification of modules that should be left out > #of the simulation, that is their genes will be simulated as unrelated > #("grey"). This can be useful when simulating several sets, in some which a module > #is present while in others it is absent. > d0 <- s_modules(n = n0, p = p, rho = 0, exposed = FALSE, + modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25), + minCor = 0.01, + maxCor = 1, + corPower = 1, + propNegativeCor = 0.3, + backgroundNoise = 0.5, + signed = FALSE, + leaveOut = 1:4) simulateDatExpr: simulating 500 genes in 5 modules. > > d1 <- s_modules(n = n1, p = p, rho = rho, exposed = TRUE, + modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25), + minCor = 0.4, + maxCor = 1, + corPower = 0.3, + propNegativeCor = 0.3, + backgroundNoise = 0.5, + signed = FALSE) simulateDatExpr: simulating 500 genes in 5 modules. > > truemodule1 <- d1$setLabels > > X <- rbind(d0$datExpr, d1$datExpr) %>% + magrittr::set_colnames(paste0("Gene", 1:p)) %>% + magrittr::set_rownames(paste0("Subject",1:n)) > > betaMainEffect <- vector("double", length = p) > > # the first nActive/2 in the 3rd block are active > betaMainEffect[which(truemodule1 %in% 3)[1:(nActive/2)]] <- runif( + nActive/2, betaMean - 0.1, betaMean + 0.1) > > # the first nActive/2 in the 4th block are active > betaMainEffect[which(truemodule1 %in% 4)[1:(nActive/2)]] <- runif( + nActive/2, betaMean+2 - 0.1, betaMean+2 + 0.1) > beta <- c(betaMainEffect, betaE) > > result <- s_generate_data_mars(p = p, X = X, + beta = beta, + binary_outcome = FALSE, + truemodule = truemodule1, + nActive = nActive, + include_interaction = FALSE, + cluster_distance = cluster_distance, + n = n, n0 = n0, + eclust_distance = Ecluster_distance, + signal_to_noise_ratio = SNR, + distance_method = distanceMethod, + cluster_method = clustMethod, + cut_method = cutMethod, + agglomeration_method = agglomerationMethod, + nPC = 1) Creating data and simulating response for MARS model Warning in k * error : Recycling array of length 1 in array-vector arithmetic is deprecated. Use c() or as.vector() instead. Calculating similarity matrices TOM calculation: adjacency.. ..will not use multithreading. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. TOM calculation: adjacency.. ..will not use multithreading. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. TOM calculation: adjacency.. ..will not use multithreading. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done. Creating CV folds from training data Calculating number of clusters based on tom using hclust with average linkage and the dynamic to determine the number of clusters ..cutHeight not given, setting it to 0.999 ===> 99% of the (truncated) height range in dendro. ..done. Error in loadNamespace(x) : there is no package called ‘factoextra’ Calls: s_generate_data_mars ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [25s/88s] ERROR Error(s) in re-building vignettes: --- re-building ‘eclust.Rmd’ using rmarkdown Quitting from lines at lines 142-168 [unnamed-chunk-6] (eclust.Rmd) Error: processing vignette 'eclust.Rmd' failed with diagnostics: there is no package called 'factoextra' --- failed re-building ‘eclust.Rmd’ SUMMARY: processing the following file failed: ‘eclust.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [12s/37s] OK * checking HTML version of manual ... [3s/10s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-Suggests/eclust.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 8:06.70, 117.71 + 13.16