############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TBSignatureProfiler.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK * this is package ‘TBSignatureProfiler’ version ‘1.17.0’ * 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 ‘TBSignatureProfiler’ 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 ... OK * checking Rd files ... NOTE checkRd: (-1) COVIDsignatures.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) COVIDsignatures.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:84: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBcommon.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:12: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:84: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:88: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:89: Lost braces in \itemize; meant \describe ? checkRd: (-1) TBsignatures.Rd:90: Lost braces in \itemize; meant \describe ? checkRd: (-1) runTBsigProfiler.Rd:51: Lost braces 51 | be of the form _. It must be set to code{TRUE} if the | ^ * 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 LazyData ... 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 bootstrapAUC 20.875 1.237 24.306 signatureROCplot_CI 10.177 0.325 11.709 signatureGeneHeatmap 10.032 0.145 11.417 SignatureQuantitative 7.311 0.377 8.523 compareAlgs 4.727 0.213 6.620 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘packagecoverage.R’ Running ‘spelling.R’ 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-3.20-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’ for details.