############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CRISPRseek_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CRISPRseek/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CRISPRseek’ version ‘1.32.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘CRISPRseek’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: extdata 9.1Mb * 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 R 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 annotateOffTargets: no visible global function definition for ‘GRanges’ annotateOffTargets: no visible global function definition for ‘exons’ annotateOffTargets: no visible global function definition for ‘seqlevels<-’ annotateOffTargets: no visible global function definition for ‘seqlevels’ annotateOffTargets: no visible global function definition for ‘GRangesList’ annotateOffTargets: no visible global function definition for ‘genes’ designPEs: no visible binding for global variable ‘ReversegRNA.cut.5prime.targetEnd’ designPEs: no visible binding for global variable ‘ReversegRNA.RT.template.length’ designPEs: no visible binding for global variable ‘ForwardgRNA.cut.5prime.targetStart’ designPEs: no visible binding for global variable ‘ForwardgRNA.RT.template.length’ filterOffTarget: no visible global function definition for ‘seqlengths’ filterOffTargetWithoutBSgenome: no visible global function definition for ‘seqlengths’ getExtendedSequence: no visible global function definition for ‘seqlengths’ getSeqFromBed: no visible global function definition for ‘seqlengths’ predictRelativeFreqIndels : : no visible global function definition for ‘predIndelFreq’ uniqueREs: no visible global function definition for ‘seqlengths’ Undefined global functions or variables: ForwardgRNA.RT.template.length ForwardgRNA.cut.5prime.targetStart GRanges GRangesList ReversegRNA.RT.template.length ReversegRNA.cut.5prime.targetEnd exons genes predIndelFreq seqlengths seqlevels seqlevels<- * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:50-52: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:62-64: Dropping empty section \note prepare_Rd: buildFeatureVectorForScoring.Rd:48-50: Dropping empty section \details prepare_Rd: buildFeatureVectorForScoring.Rd:77-79: Dropping empty section \note prepare_Rd: buildFeatureVectorForScoring.Rd:71-73: Dropping empty section \references prepare_Rd: calculategRNAEfficiency.Rd:49-51: Dropping empty section \note prepare_Rd: compare2Sequences.Rd:253-255: Dropping empty section \details prepare_Rd: compare2Sequences.Rd:295-297: Dropping empty section \note prepare_Rd: filterOffTarget.Rd:110-112: Dropping empty section \details prepare_Rd: filterOffTarget.Rd:124-126: Dropping empty section \note prepare_Rd: filtergRNA.Rd:48-50: Dropping empty section \details prepare_Rd: filtergRNA.Rd:62-64: Dropping empty section \note prepare_Rd: filtergRNA.Rd:56-58: Dropping empty section \references prepare_Rd: findgRNAs.Rd:200-202: Dropping empty section \references prepare_Rd: getOfftargetScore.Rd:73-75: Dropping empty section \note prepare_Rd: isPatternUnique.Rd:22-24: Dropping empty section \details prepare_Rd: isPatternUnique.Rd:34-36: Dropping empty section \note prepare_Rd: isPatternUnique.Rd:28-30: Dropping empty section \references prepare_Rd: isPatternUnique.Rd:40-41: Dropping empty section \seealso prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \details prepare_Rd: offTargetAnalysis.Rd:486-488: Dropping empty section \note prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:444-446: Dropping empty section \details prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:489-491: Dropping empty section \note prepare_Rd: searchHits.Rd:75-77: Dropping empty section \details prepare_Rd: searchHits.Rd:97-99: Dropping empty section \note prepare_Rd: searchHits.Rd:91-93: Dropping empty section \references prepare_Rd: searchHits2.Rd:83-85: Dropping empty section \details prepare_Rd: searchHits2.Rd:105-107: Dropping empty section \note prepare_Rd: searchHits2.Rd:99-101: Dropping empty section \references prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details prepare_Rd: translatePattern.Rd:34-36: Dropping empty section \note prepare_Rd: translatePattern.Rd:28-30: Dropping empty section \references prepare_Rd: translatePattern.Rd:40-42: Dropping empty section \seealso prepare_Rd: uniqueREs.Rd:40-42: Dropping empty section \details prepare_Rd: uniqueREs.Rd:53-55: Dropping empty section \note prepare_Rd: uniqueREs.Rd:47-49: Dropping empty section \references prepare_Rd: uniqueREs.Rd:59-60: Dropping empty section \seealso prepare_Rd: writeHits.Rd:90-92: Dropping empty section \details prepare_Rd: writeHits.Rd:102-104: Dropping empty section \note prepare_Rd: writeHits2.Rd:92-94: Dropping empty section \details prepare_Rd: writeHits2.Rd:104-106: Dropping empty section \note * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CRISPRseek-package 187.871 4.391 192.609 offTargetAnalysis 78.662 0.958 79.789 offTargetAnalysisWithoutBSgenome 62.586 0.357 63.084 compare2Sequences 10.781 0.100 10.934 annotateOffTargets 5.742 0.166 5.914 filterOffTarget 5.576 0.107 5.687 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck/00check.log’ for details.