############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTopper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTopper_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RTopper.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 ‘RTopper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RTopper’ version ‘1.51.0’ * 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 ‘RTopper’ 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) adjustPvalGSE.Rd:25: Lost braces 25 | \code{"SidakSS"}, code{"SidakSD"}, \code{"BH"} (the default), | ^ checkRd: (-1) computeDrStat.Rd:39: Lost braces 39 | \code{"dev"}{: this approach computes the score as the difference of deviances;} | ^ checkRd: (-1) computeDrStat.Rd:41-42: Lost braces 41 | \code{"aic"}{: this approach computes the score as the Akaike | ^ checkRd: (-1) computeDrStat.Rd:44: Lost braces 44 | \code{"bic"}{: this approach computes the score as the penalized likelihood ratio;} | ^ checkRd: (-1) dat.Rd:31: Lost braces 31 | \code{"dat.affy"}{: DGE obtained using Affymetrix microarrays;} | ^ checkRd: (-1) dat.Rd:33: Lost braces 33 | \code{"dat.agilent"}{: DGE obtained using Agilent microarrays;} | ^ checkRd: (-1) dat.Rd:35: Lost braces 35 | \code{"dat.cnvHarvard"}{: CNV data obtained at Harvard;} | ^ checkRd: (-1) dat.Rd:37: Lost braces 37 | \code{"dat.cnvMskcc"}{: CNV data obtained at Memorial Sloan Ketterng Cancer Center;} | ^ checkRd: (-1) fgsList.Rd:25-27: Lost braces 25 | \code{"go"}{: this is a \code{list} of 5 \code{character} vectors, | ^ checkRd: (-1) fgsList.Rd:29-31: Lost braces 29 | \code{"kegg"}{: this is a \code{list} of 5 \code{character} vectors, | ^ checkRd: (-1) gseResultsSep.Rd:30-36: Lost braces 30 | \code{"dat.affy"}{: a \code{list} of legnth two: | ^ checkRd: (-1) gseResultsSep.Rd:38-44: Lost braces 38 | \code{"dat.agilent"}{: a \code{list} of legnth two: | ^ checkRd: (-1) gseResultsSep.Rd:46-52: Lost braces 46 | \code{"dat.cnvHarvard"}{: a \code{list} of legnth two: | ^ checkRd: (-1) gseResultsSep.Rd:54-60: Lost braces 54 | \code{"dat.cnvMskcc"}{: a \code{list} of legnth two: | ^ checkRd: (-1) intScores.Rd:27-29: Lost braces 27 | \code{"integrated"}{: a \code{numeric} vector of length 500, | ^ checkRd: (-1) pheno.Rd:24: Lost braces 24 | \code{"Sample"}{: the first column contains the patients identifiers;} | ^ checkRd: (-1) pheno.Rd:26-27: Lost braces 26 | \code{"Class"}{: the second columns contain a numeric indicator | ^ checkRd: (-1) runBatchGSE.Rd:43-45: Lost braces 43 | \code{absolute}{ logical, this specifies whether the absolute values of | ^ checkRd: (-1) runBatchGSE.Rd:47-54: Lost braces 47 | \code{gseFunc}{ a function to perform GSE analysis. If not specified | ^ checkRd: (-1) runBatchGSE.Rd:58-61: Lost braces 58 | \code{type}{ character, specifies the type of statistics used to rank | ^ checkRd: (-1) runBatchGSE.Rd:63-66: Lost braces 63 | \code{alternative}{ character, defines the alternative with the | ^ checkRd: (-1) runBatchGSE.Rd:68-69: Lost braces 68 | \code{ranks.only}{ logical, if \code{TRUE} (default) only ranks will be | ^ checkRd: (-1) runBatchGSE.Rd:71-72: Lost braces 71 | \code{nsim}{ numeric, the number of randomly selected sets of genes to | ^ checkRd: (-1) sepScores.Rd:28-30: Lost braces 28 | \code{"dat.affy"}{: a \code{numeric} vector of length 500, | ^ checkRd: (-1) sepScores.Rd:32-34: Lost braces 32 | \code{"dat.agilent"}{: a \code{numeric} vector of length 500, | ^ checkRd: (-1) sepScores.Rd:36-38: Lost braces 36 | \code{"dat.cnvHarvard"}{: a \code{numeric} vector of length 500, | ^ checkRd: (-1) sepScores.Rd:40-42: Lost braces 40 | \code{"dat.cnvMskcc"}{: a \code{numeric} vector of length 500, | ^ * 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 computeDrStat 30.382 0.529 37.797 convertToDr 10.924 0.086 13.503 * 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/RTopper.Rcheck/00check.log’ for details.