############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Repitools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Repitools_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Repitools.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘Repitools/DESCRIPTION’ ... OK * this is package ‘Repitools’ version ‘1.50.0’ * 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 ‘Repitools’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... WARNING checkRd: (5) AdjustedCopyEstimate-class.Rd:16-34: \item in \describe must have non-empty label checkRd: (5) BayMethList-class.Rd:58-88: \item in \describe must have non-empty label checkRd: (-1) ChromaResults-class.Rd:25: Lost braces 25 | \code{blocks:}{\code{GRanges} of the blocks used across the genome, with their calculated RPKM} | ^ checkRd: (-1) ChromaResults-class.Rd:26: Lost braces 26 | \code{regions:}{\code{IRangesList} of regions determined to be enriched} | ^ checkRd: (-1) ChromaResults-class.Rd:27: Lost braces 27 | \code{FDRTable:}{\code{data.frame} showing the FDR at each cutoff tested} | ^ checkRd: (-1) ChromaResults-class.Rd:28: Lost braces 28 | \code{cutoff:}{The cutoff used to determine enrichment} | ^ checkRd: (5) ClusteredScoresList-class.Rd:29-50: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:57-60: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:61-64: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) ClusteredScoresList-class.Rd:75-78: \item in \describe must have non-empty label checkRd: (5) CopyEstimate-class.Rd:14-23: \item in \describe must have non-empty label checkRd: (5) GCAdjustParams-class.Rd:14-37: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:28-31: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:32-35: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:42-45: \item in \describe must have non-empty label checkRd: (5) ScoresList-class.Rd:46-49: \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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... 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 methylEst 82.351 12.784 39.756 empBayes 43.229 7.659 30.707 BayMethList-class 11.910 0.791 13.928 cpgDensityCalc 11.021 0.997 13.798 sequenceCalc 11.091 0.872 14.203 determineOffset 9.072 0.579 11.291 maskOut 8.454 0.494 10.949 findClusters 4.364 0.198 5.907 gcContentCalc 4.033 0.499 5.689 enrichmentPlot 3.568 0.324 5.206 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tests.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 WARNING See ‘/Users/biocbuild/bbs-3.19-bioc/meat/Repitools.Rcheck/00check.log’ for details.