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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RJMCMCNucleosomes_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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
* 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-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’
for details.