############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RJMCMCNucleosomes_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK * this is package ‘RJMCMCNucleosomes’ version ‘1.31.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: ‘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 ... 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 ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RJMCMCNucleosomes/libs/RJMCMCNucleosomes.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_printf’, possibly from ‘printf’ (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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’ for details.