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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CRISPRseek_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.46.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 12.7Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
* 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 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’
getOfftargetScoreBulge: no visible global function definition for
  ‘import’
predictRelativeFreqIndels : <anonymous>: no visible global function
  definition for ‘predIndelFreq’
Undefined global functions or variables:
  exons genes import 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
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
prepare_Rd: buildFeatureVectorForScoring.Rd:89-91: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:99-101: Dropping empty section \references
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: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
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: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
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: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
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:296: Lost braces; missing escapes or markup?
   296 | \item{TxDb.Rnorvegicus.UCSC.rn5.refGene} - {for rat}
       |                                            ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:297: Lost braces; missing escapes or markup?
   297 | \item{TxDb.Mmusculus.UCSC.mm10.knownGene} - {for mouse}
       |                                             ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:298: Lost braces; missing escapes or markup?
   298 | \item{TxDb.Hsapiens.UCSC.hg19.knownGene} - {for human}
       |                                            ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:299: Lost braces; missing escapes or markup?
   299 | \item{TxDb.Dmelanogaster.UCSC.dm3.ensGene} - {for Drosophila}
       |                                              ^
checkRd: (-1) offTargetAnalysisWithoutBSgenome.Rd:300: Lost braces; missing escapes or markup?
   300 | \item{TxDb.Celegans.UCSC.ce6.ensGene} - {for C.elegans}
       |                                         ^
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
prepare_Rd: uniqueREs.Rd:64-66: Dropping empty section \seealso
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 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               132.589  6.009 142.410
offTargetAnalysisWithoutBSgenome  31.807  0.417  32.768
offTargetAnalysis                 11.857  0.445  13.457
compare2Sequences                  6.758  0.209   7.587
* 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 ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.