############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HTSeqGenie_4.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HTSeqGenie.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 ‘HTSeqGenie/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HTSeqGenie’ version ‘4.36.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘HTSeqGenie’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’ ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’ ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call(ShortRead:::.set_omp_threads, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE .makePreprocessAlignPlots: no visible binding for global variable ‘data’ .plot.in.out.min.max.readlength: no visible global function definition for ‘median’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.lfqs’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.chunkid’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.subsampling_filter’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.max_nbchunks’ addHandler: no visible binding for '<<-' assignment to ‘logging.handlers’ addHandler: no visible binding for global variable ‘logging.handlers’ addHandler: no visible binding for '<<-' assignment to ‘logging.file’ buildAnyFastaGenome: no visible global function definition for ‘getSeq’ buildGenomicFeaturesFromTxDb: no visible global function definition for ‘gaps’ buildGenomicFeaturesFromTxDb: no visible global function definition for ‘ranges’ buildTP53FastaGenome: no visible global function definition for ‘getSeq’ buildTallyParam: no visible global function definition for ‘seqinfo’ computeCoverage: no visible global function definition for ‘resize’ computeCoverage: no visible global function definition for ‘coverage’ estimateCutoffs : : no visible binding for global variable ‘quantile’ getGenomeSegments: no visible global function definition for ‘seqinfo’ hashVariants: no visible global function definition for ‘ranges’ isAboveQualityThresh: no visible global function definition for ‘Views’ isAboveQualityThresh: no visible global function definition for ‘viewMeans’ listIterator.init: no visible binding for '<<-' assignment to ‘listIterator.n’ listIterator.init: no visible binding for '<<-' assignment to ‘listIterator.x’ logReset: no visible binding for '<<-' assignment to ‘logging.handlers’ logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’ logReset: no visible binding for '<<-' assignment to ‘logging.file’ loglevel: no visible binding for global variable ‘logging.loglevel’ loglevel: no visible binding for global variable ‘logging.handlers’ processChunks : tracefun: no visible binding for global variable ‘sjobs’ processChunks : tracefun: no visible binding for global variable ‘chunkid’ setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’ statCountFeatures: no visible global function definition for ‘quantile’ truncateReads: no visible global function definition for ‘subseq’ vcfStat: no visible global function definition for ‘quantile’ writeToFile: no visible binding for global variable ‘logging.file’ Undefined global functions or variables: Views chunkid coverage data gaps getSeq logging.file logging.handlers logging.loglevel median quantile ranges resize seqinfo sjobs subseq viewMeans Consider adding importFrom("stats", "median", "quantile") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup? 17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]" | ^ checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup? 18 | Setup logging file in {save_dir}/progress.log | ^ * 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 'findVariantFile.Rd': ‘dir_path’ Documented arguments not in \usage in Rd file 'logdebug.Rd': ‘...’ Documented arguments not in \usage in Rd file 'logerror.Rd': ‘...’ Documented arguments not in \usage in Rd file 'loginfo.Rd': ‘...’ Documented arguments not in \usage in Rd file 'logwarn.Rd': ‘...’ 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’