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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings consensusSeekeR_1.34.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.34.0’
* 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 ‘consensusSeekeR’ can be installed ... OK
* 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) A549_CTCF_MYJ_NarrowPeaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYJ_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_CTCF_MYJ_NarrowPeaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYJ_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYJ_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_CTCF_MYJ_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYN_NarrowPeaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYN_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_CTCF_MYN_NarrowPeaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_CTCF_MYN_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_CTCF_MYN_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_CTCF_MYN_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOSL2_01_NarrowPeaks_partial.Rd:73-74: Lost braces
    73 | \item \code{\link{A549_FOSL2_01_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_FOSL2_01_NarrowPeaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOSL2_01_Peaks_partial.Rd:74-75: Lost braces
    74 | \item \code{\link{A549_FOSL2_01_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_FOSL2_01_Peaks_partial.Rd:76-77: Lost braces
    76 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOXA1_01_NarrowPeaks_partial.Rd:71-72: Lost braces
    71 | \item \code{\link{A549_FOXA1_01_Peaks_partial}} { the associate
       |                                                 ^
checkRd: (-1) A549_FOXA1_01_NarrowPeaks_partial.Rd:73-74: Lost braces
    73 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_FOXA1_01_Peaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{A549_FOXA1_01_NarrowPeaks_partial}} { the associate
       |                                                       ^
checkRd: (-1) A549_FOXA1_01_Peaks_partial.Rd:77-78: Lost braces
    77 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFQ_NarrowPeaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFQ_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFQ_NarrowPeaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFQ_Peaks_partial.Rd:89-90: Lost braces
    89 | \item \code{\link{A549_NR3C1_CFQ_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFQ_Peaks_partial.Rd:91-92: Lost braces
    91 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFR_NarrowPeaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFR_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFR_NarrowPeaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFR_Peaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{A549_NR3C1_CFR_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFR_Peaks_partial.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFS_NarrowPeaks_partial.Rd:75-76: Lost braces
    75 | \item \code{\link{A549_NR3C1_CFS_Peaks_partial}} { the associate
       |                                                  ^
checkRd: (-1) A549_NR3C1_CFS_NarrowPeaks_partial.Rd:77-78: Lost braces
    77 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) A549_NR3C1_CFS_Peaks_partial.Rd:79-80: Lost braces
    79 | \item \code{\link{A549_NR3C1_CFS_NarrowPeaks_partial}} { the associate
       |                                                        ^
checkRd: (-1) A549_NR3C1_CFS_Peaks_partial.Rd:81-82: Lost braces
    81 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{NOrMAL_nucleosome_ranges}} { the associate
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_positions.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NOrMAL_nucleosome_ranges.Rd:80-81: Lost braces
    80 | \item \code{\link{NOrMAL_nucleosome_positions}} { the associate
       |                                                 ^
checkRd: (-1) NOrMAL_nucleosome_ranges.Rd:82-83: Lost braces
    82 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NucPosSimulator_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{NucPosSimulator_nucleosome_ranges}} { the associate
       |                                                       ^
checkRd: (-1) NucPosSimulator_nucleosome_positions.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) NucPosSimulator_nucleosome_ranges.Rd:80-81: Lost braces
    80 | \item \code{\link{NucPosSimulator_nucleosome_positions}} { the associate
       |                                                          ^
checkRd: (-1) NucPosSimulator_nucleosome_ranges.Rd:82-83: Lost braces
    82 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) PING_nucleosome_positions.Rd:79-80: Lost braces
    79 | \item \code{\link{PING_nucleosome_ranges}} { the associate
       |                                            ^
checkRd: (-1) PING_nucleosome_positions.Rd:81-82: Lost braces
    81 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) PING_nucleosome_ranges.Rd:81-82: Lost braces
    81 | \item \code{\link{PING_nucleosome_positions}} { the associate
       |                                               ^
checkRd: (-1) PING_nucleosome_ranges.Rd:83-84: Lost braces
    83 | \item \code{\link{findConsensusPeakRegions}} {for extracting regions
       |                                              ^
checkRd: (-1) consensusSeekeR-package.Rd:18-19: Lost braces
    18 | \item \code{\link{readNarrowPeakFile}} {for extracting regions and peaks
       |                                        ^
checkRd: (-1) consensusSeekeR-package.Rd:20-21: Lost braces
    20 | \item \code{\link{findConsensusPeakRegions}} { for extracting regions
       |                                              ^
* 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 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: 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.