############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IWTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IWTomics_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/IWTomics.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IWTomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IWTomics’ version ‘1.31.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘IWTomics’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: 0.99.0 First submission Cannot process chunk/lines: 0.99.11 Revised package Cannot process chunk/lines: 0.99.12 Fixed bug in plotTest and plotSummary Cannot process chunk/lines: 1.1.1 Fixed bug in IWTomicsTest statistics=variance Cannot process chunk/lines: 1.1.2 Fixed alpha Cannot process chunk/lines: 1.1.3 Fixed bug in IWTomicsData constructor Cannot process chunk/lines: 1.3.3 Citation added * 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 ... WARNING checkRd: (-1) IWTomicsData-class.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:75-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:78-79: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:87-88: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:89-91: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:92: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:93-94: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:95-96: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:97-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:103-106: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) IWTomicsData-class.Rd:108-109: Lost braces in \itemize; meant \describe ? checkRd: (5) IWTomicsData-class.Rd:122-126: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:127-170: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:177-179: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:180-182: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:183-186: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:187-189: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:190-193: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:194-196: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:197-200: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:201-204: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:205-208: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:209-211: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:212-214: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:215-217: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:218-220: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:221-223: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:224-226: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:227-229: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:230-234: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:235-237: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:238-248: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:256-261: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:269-274: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:275-280: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:281-286: \item in \describe must have non-empty label checkRd: (5) IWTomicsData-class.Rd:292-299: \item in \describe must have non-empty label * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed IWTomicsTest 38.053 1.558 39.687 IWTomics-package 7.078 1.203 8.329 IWTomicsData-class 7.316 0.049 7.377 plotSummary 3.928 1.067 5.038 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/IWTomics.Rcheck/00check.log’ for details.