############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseSignatures_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SparseSignatures.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SparseSignatures/DESCRIPTION’ ... OK * this is package ‘SparseSignatures’ version ‘2.18.0’ * 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 ‘SparseSignatures’ 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 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 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 ... NOTE import.trinucleotides.counts: no visible global function definition for ‘.’ patients.plot: no visible binding for global variable ‘Context’ patients.plot: no visible binding for global variable ‘alt’ patients.plot: no visible binding for global variable ‘patient’ patients.plot: no visible binding for global variable ‘value’ signatures.plot: no visible binding for global variable ‘Context’ signatures.plot: no visible binding for global variable ‘alt’ signatures.plot: no visible binding for global variable ‘value’ Undefined global functions or variables: . Context alt patient value * 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 nmfLassoCV 277.253 51.380 337.673 lambdaRangeBetaEvaluation 254.488 19.437 278.384 lambdaRangeAlphaEvaluation 234.232 19.966 261.816 nmfLassoBootstrap 173.751 33.527 210.116 nmfLasso 15.499 0.742 16.644 signatures.plot 8.992 0.118 9.130 startingBetaEstimation 6.340 0.125 6.474 sigAssignmentEvaluation 5.532 0.398 5.943 patients.plot 5.847 0.038 5.978 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/SparseSignatures.Rcheck/00check.log’ for details.