############################################################################## ############################################################################## ### ### 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_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Repitools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Repitools/DESCRIPTION’ ... OK * this is package ‘Repitools’ version ‘1.52.0’ * 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 ... WARNING Found the following significant warnings: hyp2f1.c:126:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hyp2f1.c:294:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hyp2f1.c:438:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] mtherr.c:77:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Repitools.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 58.442 5.630 32.863 empBayes 27.736 3.572 18.391 cpgDensityCalc 13.502 0.454 13.987 sequenceCalc 12.772 1.067 13.934 BayMethList-class 8.752 0.301 9.055 maskOut 5.895 0.586 6.490 determineOffset 5.548 0.380 5.961 * 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: 2 WARNINGs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Repitools.Rcheck/00check.log’ for details.