############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CRISPRseek_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CRISPRseek.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CRISPRseek/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CRISPRseek’ version ‘1.42.0’ * 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 ... OK * 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 12.9Mb sub-directories of 1Mb or more: extdata 12.4Mb * 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 loading without being on the library search path ... 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 ... OK * 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 ... ERROR Running examples in ‘CRISPRseek-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CRISPRseek-package > ### Title: Design of target-specific guide RNAs (gRNAs) in CRISPR-Cas9, > ### genome-editing systems > ### Aliases: CRISPRseek-package CRISPRseek > ### Keywords: package > > ### ** Examples > > library(CRISPRseek) > library("BSgenome.Hsapiens.UCSC.hg19") Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: BiocIO Loading required package: rtracklayer Attaching package: ‘rtracklayer’ The following object is masked from ‘package:BiocIO’: FileForFormat > 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") > ######## Scenario 1. Target and off-target analysis for paired gRNAs with > ######## one of the pairs overlap RE sites > results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly=TRUE, + REpatternFile =REpatternFile,findPairedgRNAOnly=TRUE, + BSgenomeName=Hsapiens, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL,max.mismatch = 1, chromToSearch = "chrX", + outputDir = outputDir,overwrite = TRUE) Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chrX ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add paired information... Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /home/biocbuild/bbs-3.18-bioc/meat/CRISPRseek.Rcheck/ > > ######## Scenario 2. Target and off-target analysis for paired gRNAs with or > ######## without RE sites > results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, + REpatternFile = REpatternFile,findPairedgRNAOnly = TRUE, + BSgenomeName = Hsapiens, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, + orgAnn = org.Hs.egSYMBOL,max.mismatch = 1, chromToSearch = "chrX", + outputDir = outputDir, overwrite = TRUE) Validating input ... Searching for gRNAs ... * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 871610 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("CRISPRseek") testing compare2Sequences search for gRNAs for input file1... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /home/biocbuild/bbs-3.18-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Nov-02-2023/ search for gRNAs for input file2... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /home/biocbuild/bbs-3.18-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Nov-02-2023/ [1] "Scoring ..." >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 2 >>> Finding all hits in sequence rs362331T ... * 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: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/CRISPRseek.Rcheck/00check.log’ for details.