############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRISPRseek.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRISPRseek_1.34.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck' * using R version 4.1.3 (2022-03-10) * 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 '1.34.2' * 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 12.9Mb 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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' predictRelativeFreqIndels : : no visible global function definition for 'predIndelFreq' Undefined global functions or variables: exons genes predIndelFreq seqlevels<- * 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:308-310: 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 ... ** running examples for arch 'i386' ... ERROR Running examples in 'CRISPRseek-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: offTargetAnalysis > ### Title: Design target-specific guide RNAs for CRISPR-Cas9 system in one > ### function > ### Aliases: offTargetAnalysis > ### Keywords: misc > > ### ** Examples > > > library(CRISPRseek) > library("BSgenome.Hsapiens.UCSC.hg19") Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: rtracklayer > library(TxDb.Hsapiens.UCSC.hg19.knownGene) Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(org.Hs.eg.db) > outputDir <- getwd() > inputFilePath <- system.file("extdata", "inputseq.fa", + package = "CRISPRseek") > REpatternFile <- system.file("extdata", "NEBenzymes.fa", + package = "CRISPRseek") > results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, + REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, + annotatePaired = FALSE, + BSgenomeName = Hsapiens, chromToSearch = "chrX", + txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, + outputDir = outputDir, overwrite = TRUE) Validating input ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Searching for gRNAs ... >>> Finding all hits in sequence chrX ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/examples_i386/ > > #### predict indels and their frequecies for target sites > > if (interactive()) + { + results <- offTargetAnalysis(inputFilePath,findgRNAsWithREcutOnly = TRUE, + findPairedgRNAOnly = FALSE, + annotatePaired = FALSE, + BSgenomeName = Hsapiens, chromToSearch = "chrX", + txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, + outputDir = outputDir, overwrite = TRUE, + predIndelFreq=TRUE, predictIndelFreq.onTargetOnly= TRUE) + + names(results$indelFreq) + head(results$indelFreq[[1]]) + ### save the indel frequences to tab delimited files, one file for each target/offtarget site. + mapply(write.table, results$indelFreq, file=paste0(names(results$indelFreq), '.xls'), sep = "\t", row.names = FALSE) + } > #### predict gRNA efficacy using CRISPRscan > featureWeightMatrixFile <- system.file("extdata", "Morenos-Mateo.csv", + package = "CRISPRseek") > > results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = TRUE, + REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, + annotatePaired = FALSE, + BSgenomeName = Hsapiens, chromToSearch = "chrX", + txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, + rule.set = "CRISPRscan", + baseBeforegRNA = 6, baseAfterPAM = 6, + featureWeightMatrixFile = featureWeightMatrixFile, + outputDir = outputDir, overwrite = TRUE) Validating input ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Searching for gRNAs ... >>> Finding all hits in sequence chrX ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/examples_i386/ > > ######## PAM is on the 5 prime side, e.g., Cpf1 > results <- offTargetAnalysis(inputFilePath = system.file("extdata", + "cpf1-2.fa", package = "CRISPRseek"), findgRNAsWithREcutOnly = FALSE, + findPairedgRNAOnly = FALSE, + annotatePaired = FALSE, + BSgenomeName = Hsapiens, + chromToSearch = "chr8", + txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL, max.mismatch = 4, + baseBeforegRNA = 8, baseAfterPAM = 26, + rule.set = "DeepCpf1", + overlap.gRNA.positions = c(19, 23), + useEfficacyFromInputSeq = FALSE, + outputDir = getwd(), + overwrite = TRUE, PAM.location = "5prime",PAM.size = 4, + PAM = "TTTN", PAM.pattern = "^TNNN", allowed.mismatch.PAM = 2, + subPAM.position = c(1,2)) Validating input ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Searching for gRNAs ... >>> Finding all hits in sequence chr8 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Warning in dir.create(outputDir) : 'C:\Users\biocbuild\bbs-3.14-bioc\meat\CRISPRseek.Rcheck\examples_i386' already exists Error: Installation of Python not found, Python bindings not loaded. Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment. Execution halted ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CRISPRseek-package 204.71 7.12 211.88 offTargetAnalysis 61.77 1.96 66.51 offTargetAnalysisWithoutBSgenome 41.38 0.08 41.47 compare2Sequences 7.91 0.10 8.00 searchHits2 4.97 0.24 5.20 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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: 1 ERROR, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRISPRseek.Rcheck/00check.log' for details.