############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CRISPRseek_1.47.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRseek.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘CRISPRseek/DESCRIPTION’ ... OK * this is package ‘CRISPRseek’ version ‘1.47.1’ * 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 ... INFO installed size is 13.0Mb sub-directories of 1Mb or more: extdata 12.5Mb * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING 'loadNamespace' or 'requireNamespace' call not declared from: ‘GeneRfold’ * 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 ‘seqlevels<-’ getOfftargetScore2: no visible binding for global variable ‘subPAM’ predictRelativeFreqIndels : : no visible global function definition for ‘predIndelFreq’ prepCasOFFinderBulge: no visible binding for global variable ‘cas_offinder_bulge’ Undefined global functions or variables: cas_offinder_bulge predIndelFreq seqlevels<- subPAM * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:64-66: Dropping empty section \details checkRd: (-1) annotateOffTargets.Rd:13-14: Lost braces 13 | \item{strand} - {strand of the off target ((+) for plus and (-) for minus | ^ checkRd: (-1) annotateOffTargets.Rd:15: Lost braces; missing escapes or markup? 15 | \item{chrom} - {chromosome of the off target} | ^ checkRd: (-1) annotateOffTargets.Rd:16-17: Lost braces 16 | \item{chromStart} - {start position of | ^ checkRd: (-1) annotateOffTargets.Rd:18: Lost braces; missing escapes or markup? 18 | \item{chromEnd} - {end position of the off target} | ^ checkRd: (-1) annotateOffTargets.Rd:19-20: Lost braces 19 | \item{name} - {gRNA | ^ checkRd: (-1) annotateOffTargets.Rd:21: Lost braces; missing escapes or markup? 21 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated} | ^ checkRd: (-1) annotateOffTargets.Rd:22: Lost braces; missing escapes or markup? 22 | \item{OffTargetSequence} - {the genomic sequence of the off target} | ^ checkRd: (-1) annotateOffTargets.Rd:23: Lost braces; missing escapes or markup? 23 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA} | ^ checkRd: (-1) annotateOffTargets.Rd:24: Lost braces; missing escapes or markup? 24 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707} | ^ checkRd: (-1) annotateOffTargets.Rd:25: Lost braces; missing escapes or markup? 25 | \item{score} - {score of the off target} | ^ checkRd: (-1) annotateOffTargets.Rd:26-28: Lost braces 26 | \item{mismatch.distance2PAM} - {a comma separated | ^ checkRd: (-1) annotateOffTargets.Rd:29-31: Lost braces 29 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means | ^ checkRd: (-1) annotateOffTargets.Rd:32-33: Lost braces 32 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes | ^ checkRd: (-1) annotateOffTargets.Rd:34-35: Lost braces 34 | \item{mean.neighbor.distance.mismatch} - {mean distance between | ^ checkRd: (-1) annotateOffTargets.Rd:45: Lost braces; missing escapes or markup? 45 | \item{TxDb.Rnorvegicus.UCSC.rn5.refGene} - {for rat} | ^ checkRd: (-1) annotateOffTargets.Rd:46: Lost braces; missing escapes or markup? 46 | \item{TxDb.Mmusculus.UCSC.mm10.knownGene} - {for mouse} | ^ checkRd: (-1) annotateOffTargets.Rd:47: Lost braces; missing escapes or markup? 47 | \item{TxDb.Hsapiens.UCSC.hg19.knownGene} - {for human} | ^ checkRd: (-1) annotateOffTargets.Rd:48: Lost braces; missing escapes or markup? 48 | \item{TxDb.Dmelanogaster.UCSC.dm3.ensGene} - {for Drosophila} | ^ checkRd: (-1) annotateOffTargets.Rd:49: Lost braces; missing escapes or markup? 49 | \item{TxDb.Celegans.UCSC.ce6.ensGene} - {for C.elegans} | ^ prepare_Rd: buildFeatureVectorForScoring.Rd:86-88: Dropping empty section \details checkRd: (-1) buildFeatureVectorForScoring.Rd:19-21: Lost braces 19 | \item{IsMismatch.posX} - {Indicator variable indicating whether this position X is | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:22-23: Lost braces 22 | \item{strand} - {strand of the | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:24-25: Lost braces 24 | \item{chrom} - {chromosome of the off | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:26: Lost braces; missing escapes or markup? 26 | \item{chromStart} - {start position of the off target} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:27-28: Lost braces 27 | \item{chromEnd} - {end | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:29: Lost braces; missing escapes or markup? 29 | \item{name} - {gRNA name} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:30-31: Lost braces 30 | \item{gRNAPlusPAM} - {gRNA sequence | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:32-33: Lost braces 32 | \item{OffTargetSequence} - {the genomic sequence of | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:34-35: Lost braces 34 | \item{n.mismatch} - {number of mismatches between the off target and | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:36-37: Lost braces 36 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:38-39: Lost braces 38 | \item{score} - {Set to 100, and will be calculated in | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:59-61: Lost braces 59 | \item{IsMismatch.posX} - {Indicator variable | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:62: Lost braces; missing escapes or markup? 62 | \item{strand} - {strand of the off target, + for plus and - for minus strand} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:63: Lost braces; missing escapes or markup? 63 | \item{chrom} - {chromosome of the off target} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:64-65: Lost braces 64 | \item{chromStart} - {start position of the off | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:66: Lost braces; missing escapes or markup? 66 | \item{chromEnd} - {end position of the off target} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:67: Lost braces; missing escapes or markup? 67 | \item{name} - {gRNA name} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:68: Lost braces; missing escapes or markup? 68 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:69: Lost braces; missing escapes or markup? 69 | \item{OffTargetSequence} - {the genomic sequence of the off target} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:70: Lost braces; missing escapes or markup? 70 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:71: Lost braces; missing escapes or markup? 71 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:72: Lost braces; missing escapes or markup? 72 | \item{score} - {score of the off target} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:73-75: Lost braces 73 | \item{mismatche.distance2PAM} - {a comma separated | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:76-77: Lost braces 76 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:78: Lost braces; missing escapes or markup? 78 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no} | ^ checkRd: (-1) buildFeatureVectorForScoring.Rd:79-80: Lost braces 79 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring | ^ checkRd: (-1) calculategRNAEfficiency.Rd:30-31: Lost braces 30 | \item{GC_LOW} - {penalty for low | ^ checkRd: (-1) calculategRNAEfficiency.Rd:32-33: Lost braces 32 | \item{GC_HIGH} - {penalty for high GC content in | ^ checkRd: (-1) calculategRNAEfficiency.Rd:34-35: Lost braces 34 | \item{G02} - {means G at second position of the | ^ checkRd: (-1) calculategRNAEfficiency.Rd:36-37: Lost braces 36 | \item{GT02} - {means GT di-nucleotides starting at 2nd position of | ^ prepare_Rd: compare2Sequences.Rd:257-259: Dropping empty section \details prepare_Rd: compare2Sequences.Rd:260-262: Dropping empty section \note prepare_Rd: filterOffTarget.Rd:154-156: Dropping empty section \details prepare_Rd: filterOffTarget.Rd:157-159: Dropping empty section \note checkRd: (-1) filterOffTarget.Rd:37: Lost braces; missing escapes or markup? 37 | \item{strand} - {strand of the off target, + for plus and - for minus strand} | ^ checkRd: (-1) filterOffTarget.Rd:38: Lost braces; missing escapes or markup? 38 | \item{chrom} - {chromosome of the off target} | ^ checkRd: (-1) filterOffTarget.Rd:39: Lost braces; missing escapes or markup? 39 | \item{chromStart} - {start position of the offtarget} | ^ checkRd: (-1) filterOffTarget.Rd:40: Lost braces; missing escapes or markup? 40 | \item{chromEnd} - {end position of the offtarget} | ^ checkRd: (-1) filterOffTarget.Rd:41: Lost braces; missing escapes or markup? 41 | \item{name} - {gRNA name} | ^ checkRd: (-1) filterOffTarget.Rd:42: Lost braces; missing escapes or markup? 42 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated} | ^ checkRd: (-1) filterOffTarget.Rd:43: Lost braces; missing escapes or markup? 43 | \item{OffTargetSequence} - {the genomic sequence of the off target} | ^ checkRd: (-1) filterOffTarget.Rd:44: Lost braces; missing escapes or markup? 44 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA} | ^ checkRd: (-1) filterOffTarget.Rd:45: Lost braces; missing escapes or markup? 45 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707} | ^ checkRd: (-1) filterOffTarget.Rd:46: Lost braces; missing escapes or markup? 46 | \item{score} - {score of the off target} | ^ checkRd: (-1) filterOffTarget.Rd:47-49: Lost braces 47 | \item{mismatch.distance2PAM} - {a comma separated | ^ checkRd: (-1) filterOffTarget.Rd:50-52: Lost braces 50 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means | ^ checkRd: (-1) filterOffTarget.Rd:53-54: Lost braces 53 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes | ^ checkRd: (-1) filterOffTarget.Rd:55-56: Lost braces 55 | \item{mean.neighbor.distance.mismatch} - {mean distance between | ^ checkRd: (-1) filterOffTarget.Rd:101: Lost braces; missing escapes or markup? 101 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19} | ^ checkRd: (-1) filterOffTarget.Rd:102: Lost braces; missing escapes or markup? 102 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10} | ^ checkRd: (-1) filterOffTarget.Rd:103: Lost braces; missing escapes or markup? 103 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6} | ^ checkRd: (-1) filterOffTarget.Rd:104: Lost braces; missing escapes or markup? 104 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5} | ^ checkRd: (-1) filterOffTarget.Rd:105: Lost braces; missing escapes or markup? 105 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3} | ^ prepare_Rd: filtergRNAs.Rd:48-50: Dropping empty section \details prepare_Rd: filtergRNAs.Rd:51-53: Dropping empty section \note prepare_Rd: filtergRNAs.Rd:74-76: Dropping empty section \references prepare_Rd: findgRNAs.Rd:319-321: Dropping empty section \references prepare_Rd: getOfftargetScore.Rd:79-81: Dropping empty section \note checkRd: (-1) getOfftargetScore.Rd:17-19: Lost braces 17 | \item{IsMismatch.posX} - {Indicator variable | ^ checkRd: (-1) getOfftargetScore.Rd:20: Lost braces; missing escapes or markup? 20 | \item{strand} - {strand of the off target, + for plus and - for minus strand} | ^ checkRd: (-1) getOfftargetScore.Rd:21: Lost braces; missing escapes or markup? 21 | \item{chrom} - {chromosome of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:22-23: Lost braces 22 | \item{chromStart} - {start position of the off | ^ checkRd: (-1) getOfftargetScore.Rd:24: Lost braces; missing escapes or markup? 24 | \item{chromEnd} - {end position of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:25: Lost braces; missing escapes or markup? 25 | \item{name} - {gRNA name} | ^ checkRd: (-1) getOfftargetScore.Rd:26: Lost braces; missing escapes or markup? 26 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated} | ^ checkRd: (-1) getOfftargetScore.Rd:27: Lost braces; missing escapes or markup? 27 | \item{OffTargetSequence} - {the genomic sequence of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:28: Lost braces; missing escapes or markup? 28 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA} | ^ checkRd: (-1) getOfftargetScore.Rd:29: Lost braces; missing escapes or markup? 29 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707} | ^ checkRd: (-1) getOfftargetScore.Rd:30: Lost braces; missing escapes or markup? 30 | \item{score} - {score of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:31-33: Lost braces 31 | \item{mismatche.distance2PAM} - {a comma separated | ^ checkRd: (-1) getOfftargetScore.Rd:34-35: Lost braces 34 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means | ^ checkRd: (-1) getOfftargetScore.Rd:36: Lost braces; missing escapes or markup? 36 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no} | ^ checkRd: (-1) getOfftargetScore.Rd:37-38: Lost braces 37 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring | ^ checkRd: (-1) getOfftargetScore.Rd:49-50: Lost braces 49 | {strand} - {strand of the match, + for plus and | ^ checkRd: (-1) getOfftargetScore.Rd:51: Lost braces; missing escapes or markup? 51 | \item{chrom} - {chromosome of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:52-53: Lost braces 52 | \item{chromStart} - {start | ^ checkRd: (-1) getOfftargetScore.Rd:54: Lost braces; missing escapes or markup? 54 | \item{chromEnd} - {end position of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:55: Lost braces; missing escapes or markup? 55 | \item{name} - {gRNA name} | ^ checkRd: (-1) getOfftargetScore.Rd:56: Lost braces; missing escapes or markup? 56 | \item{gRNAPlusPAM} - {gRNA sequence with PAM sequence concatenated} | ^ checkRd: (-1) getOfftargetScore.Rd:57: Lost braces; missing escapes or markup? 57 | \item{OffTargetSequence} - {the genomic sequence of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:58: Lost braces; missing escapes or markup? 58 | \item{n.mismatch} - {number of mismatches between the off target and the gRNA} | ^ checkRd: (-1) getOfftargetScore.Rd:59: Lost braces; missing escapes or markup? 59 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707} | ^ checkRd: (-1) getOfftargetScore.Rd:60: Lost braces; missing escapes or markup? 60 | \item{score} - {score of the off target} | ^ checkRd: (-1) getOfftargetScore.Rd:61-63: Lost braces 61 | \item{mismatch.distance2PAM} - {a comma separated | ^ checkRd: (-1) getOfftargetScore.Rd:64-65: Lost braces 64 | \item{alignment} - {alignment between gRNA and off target, e.g., ......G..C.......... means | ^ checkRd: (-1) getOfftargetScore.Rd:66: Lost braces; missing escapes or markup? 66 | \item{NGG} - {this off target contains canonical PAM or not, 1 for yes and 0 for no} | ^ checkRd: (-1) getOfftargetScore.Rd:67-68: Lost braces 67 | \item{mean.neighbor.distance.mismatch} - {mean distance between neighboring | ^ prepare_Rd: isPatternUnique.Rd:23-25: Dropping empty section \details prepare_Rd: isPatternUnique.Rd:26-28: Dropping empty section \note prepare_Rd: isPatternUnique.Rd:35-37: Dropping empty section \references prepare_Rd: offTargetAnalysis.Rd:461-463: Dropping empty section \details prepare_Rd: offTargetAnalysis.Rd:464-466: 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 checkRd: (-1) searchHits.Rd:74-75: Lost braces 74 | \item{IsMismatch.posX} - {indicator variable indicating | ^ checkRd: (-1) searchHits.Rd:76-77: Lost braces 76 | \item{strand} - {strand of | ^ checkRd: (-1) searchHits.Rd:78-79: Lost braces 78 | \item{chrom} - {chromosome of the off | ^ checkRd: (-1) searchHits.Rd:80: Lost braces; missing escapes or markup? 80 | \item{chromStart} - {start position of the off target} | ^ checkRd: (-1) searchHits.Rd:81-82: Lost braces 81 | \item{chromEnd} - {end | ^ checkRd: (-1) searchHits.Rd:83: Lost braces; missing escapes or markup? 83 | \item{name} - {gRNA name} | ^ checkRd: (-1) searchHits.Rd:84-85: Lost braces 84 | \item{gRNAPlusPAM} - {gRNA sequence | ^ checkRd: (-1) searchHits.Rd:86-87: Lost braces 86 | \item{OffTargetSequence} - {the genomic sequence of | ^ checkRd: (-1) searchHits.Rd:88-89: Lost braces 88 | \item{n.mismatch} - {number of mismatches between the off target and | ^ checkRd: (-1) searchHits.Rd:90-91: Lost braces 90 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., | ^ checkRd: (-1) searchHits.Rd:92-93: Lost braces 92 | \item{score} - {set to 100, and will be updated in | ^ 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 checkRd: (-1) searchHits2.Rd:90-92: Lost braces 90 | \item{IsMismatch.posX} - {indicator variable indicating | ^ checkRd: (-1) searchHits2.Rd:93-94: Lost braces 93 | \item{strand} - {strand of | ^ checkRd: (-1) searchHits2.Rd:95-96: Lost braces 95 | \item{chrom} - {chromosome of the off | ^ checkRd: (-1) searchHits2.Rd:97: Lost braces; missing escapes or markup? 97 | \item{chromStart} - {start position of the off target} | ^ checkRd: (-1) searchHits2.Rd:98-99: Lost braces 98 | \item{chromEnd} - {end | ^ checkRd: (-1) searchHits2.Rd:100: Lost braces; missing escapes or markup? 100 | \item{name} - {gRNA name} | ^ checkRd: (-1) searchHits2.Rd:101-102: Lost braces 101 | \item{gRNAPlusPAM} - {gRNA sequence | ^ checkRd: (-1) searchHits2.Rd:103-104: Lost braces 103 | \item{OffTargetSequence} - {the genomic sequence of | ^ checkRd: (-1) searchHits2.Rd:105-106: Lost braces 105 | \item{n.mismatch} - {number of mismatches between the off target and | ^ checkRd: (-1) searchHits2.Rd:107-108: Lost braces 107 | \item{forViewInUCSC} - {string for viewing in UCSC genome browser, e.g., | ^ checkRd: (-1) searchHits2.Rd:109-110: Lost braces 109 | \item{score} - {set to 100, and will be updated in | ^ 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 checkRd: (-1) uniqueREs.Rd:30: Lost braces; missing escapes or markup? 30 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19} | ^ checkRd: (-1) uniqueREs.Rd:31: Lost braces; missing escapes or markup? 31 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10} | ^ checkRd: (-1) uniqueREs.Rd:32: Lost braces; missing escapes or markup? 32 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6} | ^ checkRd: (-1) uniqueREs.Rd:33: Lost braces; missing escapes or markup? 33 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5} | ^ checkRd: (-1) uniqueREs.Rd:34: Lost braces; missing escapes or markup? 34 | \item{BSgenome.Drerio.UCSC.danRer7} - {for Zv9} | ^ checkRd: (-1) uniqueREs.Rd:35: Lost braces; missing escapes or markup? 35 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3} | ^ 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 checkRd: (-1) writeHits2.Rd:68: Lost braces; missing escapes or markup? 68 | \item{BSgenome.Hsapiens.UCSC.hg19} - {for hg19} | ^ checkRd: (-1) writeHits2.Rd:69: Lost braces; missing escapes or markup? 69 | \item{BSgenome.Mmusculus.UCSC.mm10} - {for mm10} | ^ checkRd: (-1) writeHits2.Rd:70: Lost braces; missing escapes or markup? 70 | \item{BSgenome.Celegans.UCSC.ce6} - {for ce6} | ^ checkRd: (-1) writeHits2.Rd:71: Lost braces; missing escapes or markup? 71 | \item{BSgenome.Rnorvegicus.UCSC.rn5} - {for rn5} | ^ checkRd: (-1) writeHits2.Rd:72: Lost braces; missing escapes or markup? 72 | \item{BSgenome.Drerio.UCSC.danRer7} - {for Zv9} | ^ checkRd: (-1) writeHits2.Rd:73: Lost braces; missing escapes or markup? 73 | \item{BSgenome.Dmelanogaster.UCSC.dm3} - {for dm3} | ^ * 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: findgRNAs > ### Title: Find potential gRNAs > ### Aliases: findgRNAs > ### Keywords: misc > > ### ** Examples > > > # Example1: DNAStringSet as input, only output paired gRNAs > inputSeq <- DNAStringSet(paste0("CCAGTTTGTGGATCCTGCTCTGGTGTC", + "CTCCACACCAGAATCAGGGATCGAAAA", + "CTCATCAGTCGATGCGAGTCATCTAAA", + "TTCCGATCAATTTCACACTTTAAACG")) > findgRNAs(inputFilePath = inputSeq, + findPairedgRNAOnly = TRUE, + pairOutputFile = "test_findgRNAs1.xlsx", + PAM.size = 3L, + gRNA.size = 20L, + overlap.gRNA.positions = c(17L,18L), + PBS.length = 15, + corrected.seq = "T", + RT.template.pattern = "D$", + RT.template.length = 8:30, + targeted.seq.length.change = 0, + bp.after.target.end = 15, + target.start = 46, + target.end = 46, + paired.orientation = "PAMin", + min.gap = 20, + max.gap = 90, + primeEditing = TRUE) DNAStringSet object of length 3: width seq names [1] 23 GTGTCCTCCACACCAGAATCAGG NA_gR39f [2] 23 TGTCCTCCACACCAGAATCAGGG NA_gR40f [3] 23 GTTTAAAGTGTGAAATTGATCGG NA_gR90r > > # Example2: FASTA as input, only output paired gRNAs > findgRNAs(inputFilePath = system.file("extdata", + "inputseq.fa", + package = "CRISPRseek"), + findPairedgRNAOnly = TRUE, + pairOutputFile = "test_findgRNAs2.xlsx") DNAStringSet object of length 3: width seq names [1] 23 GTGTCCTCCACACCAGAATCAGG Hsap_GATA1_ex2_gR39f [2] 23 TGTCCTCCACACCAGAATCAGGG Hsap_GATA1_ex2_gR40f [3] 23 CCAGAGCAGGATCCACAAACTGG Hsap_GATA1_ex2_gR7r > > # Example3: predict gRNA efficacy using CRISPRscan > featureWeightMatrixFile <- system.file("extdata", + "Morenos-Mateo.csv", + package = "CRISPRseek") > findgRNAs(inputFilePath = system.file("extdata", + "testCRISPRscan.fa", + package = "CRISPRseek"), + pairOutputFile = "test_findgRNAs3.xlsx", + findPairedgRNAOnly = FALSE, + calculategRNAEfficacy= TRUE, + rule.set = "CRISPRscan", + baseBeforegRNA = 6, + baseAfterPAM = 6, + featureWeightMatrixFile = featureWeightMatrixFile, + efficacyFile = "testCRISPRscanEfficacy.xlsx") DNAStringSet object of length 10: width seq names [1] 23 ATCCATGGAGCAGTACCAGGTGG gRNA1test:crisprS... [2] 23 GGAGCAGTACCAGGTGGACTCGG gRNA1test:crisprS... [3] 23 GTCCACCTGGTACTGCTCCATGG gRNA1test:crisprS... [4] 23 AGAGGACTGTTTGGACAACATGG gRNA2test:risprSc... [5] 23 CTGTTTGGACAACATGGAAGCGG gRNA2test:risprSc... [6] 23 AACATGGAAGCGGCTGTTTTTGG gRNA3test-crisprS... [7] 23 GGAAGCGGCTGTTTTTGGAGTGG gRNA3test-crisprS... [8] 23 AGCGGCTGTTTTTGGAGTGGTGG gRNA3test-crisprS... [9] 23 GGAAGCGGCTGTTTTTGGAGTGG gRNA4test:crisprS... [10] 23 AGCGGCTGTTTTTGGAGTGGTGG gRNA4test:crisprS... > > # Example 4: predict gRNA efficacy using DeepCpf1 > findgRNAs(inputFilePath = system.file("extdata", + "cpf1.fa", + package = "CRISPRseek"), + findPairedgRNAOnly = FALSE, + pairOutputFile = "test_findgRNAs_cpf1.xlsx", + PAM = "TTTN", + PAM.location = "5prime", + PAM.size = 4, + overlap.gRNA.positions = c(19, 23), + baseBeforegRNA = 8, + baseAfterPAM = 26, + calculategRNAEfficacy = TRUE, + rule.set = "DeepCpf1", + efficacyFile = "testcpf1Efficacy.xlsx") Error: Valid installation of TensorFlow not found. Python environments searched for 'tensorflow' package: /usr/bin/python3.12 Python exception encountered: Traceback (most recent call last): File "/home/biocbuild/bbs-3.21-bioc/R/site-library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook return _run_hook(name, _hook) ^^^^^^^^^^^^^^^^^^^^^^ File "/home/biocbuild/bbs-3.21-bioc/R/site-library/reticulate/python/rpytools/loader.py", line 96, in _run_hook module = hook() ^^^^^^ File "/home/biocbuild/bbs-3.21-bioc/R/site-library/reticulate/python/rpytools/loader.py", line 120, in _hook return _find_and_load(name, import_) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/biocbuild/.virtualenvs/r-reticulate/lib/python3.12/site-packages/tensorflow/__init__.py", line 30, in import distutils as _distutils File "/home/biocbuild/bbs-3.21-bioc/R/site-library/reticulate/python/rpytools/loader.py", line 122, in Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed compare2Sequences 7.280 0.476 7.748 annotateOffTargets 5.879 0.352 6.492 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRseek.Rcheck/00check.log’ for details.