############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Repitools.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Repitools_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Repitools.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methylEst 85.005 9.070 27.922 empBayes 46.101 6.341 24.550 cpgDensityCalc 11.089 0.310 11.463 sequenceCalc 11.046 0.188 11.251 BayMethList-class 9.778 0.172 9.972 determineOffset 7.085 0.036 7.134 maskOut 6.672 0.076 6.760 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/Repitools.Rcheck/00check.log’ for details.