############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CRISPRseek.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CRISPRseek_1.35.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CRISPRseek.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CRISPRseek/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CRISPRseek' version '1.35.6' * 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 whether package 'CRISPRseek' can be installed ... OK * checking installed package size ... NOTE installed size is 12.8Mb sub-directories of 1Mb or more: extdata 12.1Mb * 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 'exons' annotateOffTargets: no visible global function definition for 'seqlevels<-' annotateOffTargets: no visible global function definition for 'genes' getOfftargetScore2: no visible binding for global variable 'subPAM' predictRelativeFreqIndels : : no visible global function definition for 'predIndelFreq' Undefined global functions or variables: exons genes predIndelFreq seqlevels<- subPAM * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:67-69: Dropping empty section \note prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references prepare_Rd: compare2Sequences.Rd:263-265: Dropping empty section \details prepare_Rd: compare2Sequences.Rd:266-268: Dropping empty section \note prepare_Rd: filterOffTarget.Rd:151-153: Dropping empty section \details prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \note prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note prepare_Rd: filtergRNAs.Rd:70-72: Dropping empty section \references prepare_Rd: findgRNAs.Rd:307-309: Dropping empty section \references prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note prepare_Rd: isPatternUnique.Rd:37-39: Dropping empty section \references prepare_Rd: isPatternUnique.Rd:40-42: Dropping empty section \seealso prepare_Rd: offTargetAnalysis.Rd:438-440: Dropping empty section \details prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \note prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:440-442: Dropping empty section \details prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:443-445: Dropping empty section \note prepare_Rd: searchHits.Rd:99-101: Dropping empty section \details prepare_Rd: searchHits.Rd:102-104: Dropping empty section \note prepare_Rd: searchHits.Rd:130-132: Dropping empty section \references prepare_Rd: searchHits2.Rd:116-118: Dropping empty section \details prepare_Rd: searchHits2.Rd:119-121: Dropping empty section \note prepare_Rd: searchHits2.Rd:152-154: Dropping empty section \references prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details prepare_Rd: translatePattern.Rd:25-27: Dropping empty section \note prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \references prepare_Rd: translatePattern.Rd:36-38: Dropping empty section \seealso prepare_Rd: uniqueREs.Rd:46-48: Dropping empty section \details prepare_Rd: uniqueREs.Rd:49-51: Dropping empty section \note prepare_Rd: uniqueREs.Rd:61-63: Dropping empty section \references prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso prepare_Rd: writeHits.Rd:89-91: Dropping empty section \details prepare_Rd: writeHits.Rd:92-94: Dropping empty section \note prepare_Rd: writeHits2.Rd:99-101: Dropping empty section \details prepare_Rd: writeHits2.Rd:102-104: 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CRISPRseek-package 159.75 14.39 174.41 offTargetAnalysisWithoutBSgenome 32.31 0.22 32.58 offTargetAnalysis 10.91 0.75 11.66 compare2Sequences 5.61 0.04 5.78 searchHits2 4.47 0.72 5.42 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' Running 'testthat.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: 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/CRISPRseek.Rcheck/00check.log' for details.