############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsSampleSize.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsSampleSize_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.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 ‘MSstatsSampleSize/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsSampleSize’ version ‘1.16.0’ * 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 ‘MSstatsSampleSize’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'MSstatsSampleSize' is deprecated and will be removed from See ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.Rcheck/00install.out’ for details. * 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 ... WARNING Functions or methods with usage in documentation object '.classification' but not in code: ‘.classification’ * 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 ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress classification_results.rda 1.8Mb 1.3Mb xz simulated_datasets.rda 656Kb 511Kb xz variance_estimation.rda 690Kb 321Kb xz * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘MSstatsSampleSize-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: designSampleSizeClassification > ### Title: Estimate the mean predictive accuracy and mean protein > ### importance over all the simulated datasets > ### Aliases: designSampleSizeClassification > > ### ** Examples > > data(OV_SRM_train) > data(OV_SRM_train_annotation) > > # num_simulations = 10: simulate 10 times > # expected_FC = "data": fold change estimated from OV_SRM_train > # select_simulated_proteins = "proportion": > # select the simulated proteins based on the proportion of total proteins > # simulate_valid = FALSE: use input OV_SRM_train as validation set > # valid_samples_per_group = 50: 50 samples per condition > simulated_datasets <- simulateDataset(data = OV_SRM_train, + annotation = OV_SRM_train_annotation, + num_simulations = 10, + expected_FC = "data", + list_diff_proteins = NULL, + select_simulated_proteins = "proportion", + protein_proportion = 1.0, + protein_number = 1000, + samples_per_group = 50, + simulate_valid = FALSE, + valid_samples_per_group = 50) Preparing variance analysis... Variance analysis completed. Preparing simulation... Size of training data to simulate: 100 Number of proteins to simulate: 67 Start to run the simulation... Simulation: 1 Simulation: 2 Simulation: 3 Simulation: 4 Simulation: 5 Simulation: 6 Simulation: 7 Simulation: 8 Simulation: 9 Simulation: 10 Simulation completed. > > # run classification on simulated datasets without parallel computation > classification_results <- designSampleSizeClassification(simulations = simulated_datasets, + parallel = FALSE) classifier: rf Start to train classifier... Error: Required packages are missing: randomForest Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test-designSampleSizeClassification.R:6:5'): designSampleSizeClassification works ── Error: Required packages are missing: randomForest Backtrace: ▆ 1. └─MSstatsSampleSize::designSampleSizeClassification(simulations = MSstatsSampleSize::simulated_datasets) at test-designSampleSizeClassification.R:6:5 2. └─base::lapply(...) 3. └─MSstatsSampleSize (local) FUN(X[[i]], ...) 4. └─MSstatsSampleSize:::.classificationModel(x = x, y = y, classifier = classifier) 5. ├─caret::train(...) 6. └─caret:::train.default(...) 7. └─caret::checkInstall(models$library) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MSstatsSampleSize.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘MSstatsSampleSize.Rmd’ ... Simulation completed. > classification_results <- designSampleSizeClassification(simulations = simulated_datasets, + parallel = FALSE) classifier: rf Start to train classifier... When sourcing ‘MSstatsSampleSize.R’: Error: Required packages are missing: randomForest Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: ... --- re-building ‘MSstatsSampleSize.Rmd’ using rmarkdown Quitting from lines at lines 213-217 [unnamed-chunk-7] (MSstatsSampleSize.Rmd) Error: processing vignette 'MSstatsSampleSize.Rmd' failed with diagnostics: Required packages are missing: randomForest --- failed re-building ‘MSstatsSampleSize.Rmd’ SUMMARY: processing the following file failed: ‘MSstatsSampleSize.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 3 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsSampleSize.Rcheck/00check.log’ for details.