############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RJMCMCNucleosomes_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK * this is package ‘RJMCMCNucleosomes’ version ‘1.29.0’ * package encoding: UTF-8 * 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 ‘RJMCMCNucleosomes’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 ... NOTE checkRd: (-1) RJMCMCNucleosomes-package.Rd:16-17: Lost braces 16 | \item \code{\link{rjmcmc}} { for profiling of nucleosome positions for a | ^ checkRd: (-1) RJMCMCNucleosomes-package.Rd:18-20: Lost braces 18 | \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions | ^ checkRd: (-1) RJMCMCNucleosomes-package.Rd:21-23: Lost braces 21 | \item \code{\link{segmentation}} { for spliting a \code{GRanges} | ^ checkRd: (-1) RJMCMCNucleosomes-package.Rd:24-25: Lost braces 24 | \item \code{\link{postTreatment}} { for merging closely positioned | ^ checkRd: (-1) RJMCMCNucleosomes-package.Rd:26-27: Lost braces 26 | \item \code{\link{mergeRDSFiles}} { for merging nucleosome information | ^ checkRd: (-1) RJMCMCNucleosomes-package.Rd:28-29: Lost braces 28 | \item \code{\link{plotNucleosomes}} { for generating a graph containing | ^ checkRd: (-1) RJMCMC_result.Rd:61: Lost braces; missing escapes or markup? 61 | \item \code{\link{rjmcmc}} {for profiling of nucleosome positions} | ^ checkRd: (-1) RJMCMC_result.Rd:62-64: Lost braces 62 | \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions | ^ checkRd: (-1) RJMCMC_result.Rd:65-67: Lost braces 65 | \item \code{\link{segmentation}} { for spliting a \code{GRanges} | ^ checkRd: (-1) RJMCMC_result.Rd:68-69: Lost braces 68 | \item \code{\link{postTreatment}} { for merging closely positioned | ^ checkRd: (-1) RJMCMC_result.Rd:70-71: Lost braces 70 | \item \code{\link{mergeRDSFiles}} { for merging nucleosome information | ^ checkRd: (-1) RJMCMC_result.Rd:72-73: Lost braces 72 | \item \code{\link{plotNucleosomes}} { for generating a graph containing | ^ checkRd: (-1) reads_demo_01.Rd:31: Lost braces; missing escapes or markup? 31 | \item \code{\link{rjmcmc}} {for profiling of nucleosome positions} | ^ checkRd: (-1) reads_demo_02.Rd:33: Lost braces; missing escapes or markup? 33 | \item \code{\link{rjmcmc}} {for profiling of nucleosome positions} | ^ checkRd: (-1) reads_demo_02.Rd:34-36: Lost braces 34 | \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions | ^ checkRd: (-1) reads_demo_02.Rd:37-39: Lost braces 37 | \item \code{\link{segmentation}} { for spliting a \code{GRanges} | ^ checkRd: (-1) reads_demo_02.Rd:40-41: Lost braces 40 | \item \code{\link{postTreatment}} { for merging closely positioned | ^ checkRd: (-1) reads_demo_02.Rd:42-43: Lost braces 42 | \item \code{\link{mergeRDSFiles}} { for merging nucleosome information | ^ checkRd: (-1) reads_demo_02.Rd:44-45: Lost braces 44 | \item \code{\link{plotNucleosomes}} { for generating a graph containing | ^ * 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 ... NOTE Documented arguments not in \usage in Rd file 'runCHR.Rd': ‘kMax’ ‘minInterval’ ‘maxInterval’ ‘maxLength’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/RJMCMCNucleosomes/libs/RJMCMCNucleosomes.so’: Found ‘__printf_chk’, possibly from ‘printf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’ for details.