############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IWTomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings IWTomics_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IWTomics.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘IWTomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IWTomics’ version ‘1.23.0’ * 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 ‘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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.IWTomicsData See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... WARNING 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed IWTomicsTest 54.454 0.584 55.389 IWTomicsData-class 11.097 0.120 11.243 IWTomics-package 8.232 0.515 8.753 plotSummary 4.762 0.612 5.375 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘IWTomics.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/IWTomics.Rcheck/00check.log’ for details.