############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hiReadsProcessor_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/hiReadsProcessor.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK * this is package ‘hiReadsProcessor’ version ‘1.42.0’ * 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 ... 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 ‘hiReadsProcessor’ 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 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 ... NOTE chunkize: no visible global function definition for ‘breakInChunks’ chunkize: no visible global function definition for ‘detectCores’ clusterSites : : no visible binding for global variable ‘queryHits’ clusterSites: no visible binding for global variable ‘clusteredValue’ clusterSites: no visible binding for global variable ‘clusteredValue.freq’ crossOverCheck: no visible binding for global variable ‘queryHits’ decodeByBarcode: no visible global function definition for ‘metadata<-’ decodeByBarcode: no visible global function definition for ‘metadata’ extractSeqs : : no visible global function definition for ‘metadata’ extractSeqs : : : : no visible global function definition for ‘IRanges’ extractSeqs : : : no visible global function definition for ‘IRanges’ findBarcodes: no visible global function definition for ‘metadata<-’ findBarcodes: no visible global function definition for ‘metadata’ findIntegrations: no visible global function definition for ‘fasta.info’ findIntegrations : : no visible global function definition for ‘IRanges’ findVector : : no visible global function definition for ‘IRanges’ pairUpAlignments : : no visible binding for global variable ‘queryHits’ pairwiseAlignSeqs: no visible global function definition for ‘IRangesList’ pairwiseAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRangesList’ pslToRangedObject: no visible global function definition for ‘IRanges’ read.BAMasPSL: no visible global function definition for ‘ScanBamParam’ read.BAMasPSL: no visible global function definition for ‘scanBamFlag’ read.BAMasPSL: no visible global function definition for ‘DataFrame’ read.SeqFolder: no visible global function definition for ‘SimpleList’ read.psl: no visible global function definition for ‘mclapply’ read.psl : : no visible binding for global variable ‘matches’ read.psl : : no visible binding for global variable ‘misMatches’ read.psl : : no visible binding for global variable ‘qBaseInsert’ read.psl : : no visible binding for global variable ‘tBaseInsert’ read.psl: no visible binding for global variable ‘matches’ read.psl: no visible binding for global variable ‘misMatches’ read.psl: no visible binding for global variable ‘qBaseInsert’ read.psl: no visible binding for global variable ‘tBaseInsert’ read.sampleInfo: no visible global function definition for ‘SimpleList’ splitSeqsToFiles: no visible global function definition for ‘fasta.info’ vpairwiseAlignSeqs: no visible global function definition for ‘Rle’ vpairwiseAlignSeqs: no visible global function definition for ‘runLength’ vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’ vpairwiseAlignSeqs: no visible global function definition for ‘runValue’ Undefined global functions or variables: DataFrame IRanges IRangesList Rle ScanBamParam SimpleList breakInChunks clusteredValue clusteredValue.freq detectCores fasta.info matches mclapply metadata metadata<- misMatches qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert * checking Rd files ... OK * 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 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/hiReadsProcessor.Rcheck/00check.log’ for details.