############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ...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 ‘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 ‘/home/biocbuild/bbs-3.20-bioc/meat/consensusSeekeR.Rcheck/00check.log’ for details.