############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FCBF.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FCBF_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FCBF.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘FCBF/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FCBF’ version ‘2.10.0’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FCBF’ can be installed ... OK * checking installed package size ... 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 startup messages can be suppressed ... 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 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fcbf 22.792 0.217 23.010 get_ig_for_feature_table_and_vector 15.393 0.060 15.592 scDengue 15.094 0.084 15.178 get_su_for_feature_table_and_vector 10.740 0.172 11.332 su_plot 8.793 0.032 8.824 discretize_exprs 7.850 0.360 8.289 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘FCBF-Vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘FCBF-Vignette.Rmd’ ... > control <- trainControl(method = "cv", number = 5, + classProbs = TRUE, summaryFunction = twoClassSummary) > svm_fcbf <- train(target_variable ~ ., metric = "ROC", + data = dataset_fcbf, method = "svmRadial", trControl = control) When sourcing ‘FCBF-Vignette.R’: Error: Required packages are missing: kernlab Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: ... --- re-building ‘FCBF-Vignette.Rmd’ using rmarkdown Quitting from lines at lines 178-205 [unnamed-chunk-10] (FCBF-Vignette.Rmd) Error: processing vignette 'FCBF-Vignette.Rmd' failed with diagnostics: Required packages are missing: kernlab --- failed re-building ‘FCBF-Vignette.Rmd’ SUMMARY: processing the following file failed: ‘FCBF-Vignette.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/FCBF.Rcheck/00check.log’ for details.