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### Running command:
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### /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
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRseek.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 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 : <anonymous>: 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:324-326: 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
offTargetAnalysis 70.326 5.325 75.216
compare2Sequences 8.210 0.796 8.992
annotateOffTargets 7.847 0.537 8.386
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.