* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/bisect.Rcheck’ * using R Under development (unstable) (2022-05-11 r82344) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘bisect/DESCRIPTION’ ... OK * this is package ‘bisect’ version ‘0.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘sirt’ * 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 ‘bisect’ can be installed ... 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 R 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 use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... 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 ... ERROR Running examples in ‘bisect-Ex.R’ failed The error most likely occurred in: > ### Name: bisect_semi_suprevised > ### Title: Add together two numbers. > ### Aliases: bisect_semi_suprevised > > ### ** Examples > > ## Randomly choose samples to be used as known > n_known_samples <- 50 > known_samples_indices <- sample.int(nrow(baseline_GSE40279), size = n_known_samples) > known_samples <- as.matrix(baseline_GSE40279[known_samples_indices, ]) > > ## Fit a dirichlet distribution to known samples to use as prior > fit_dirichlet <- sirt::dirichlet.mle(as.matrix(known_samples)) Error in loadNamespace(x) : there is no package called ‘sirt’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... 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 See ‘/data/gannet/ripley/R/packages/tests-Suggests/bisect.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 0:44.10, 27.01 + 5.39