Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 455/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CRISPRseek 1.45.0 (landing page) Lihua Julie Zhu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CRISPRseek package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: CRISPRseek |
Version: 1.45.0 |
Command: /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_1.45.0.tar.gz |
StartedAt: 2024-08-26 20:34:31 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:47:34 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 782.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CRISPRseek.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CRISPRseek/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CRISPRseek’ version ‘1.45.0’ * 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 12.7Mb 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 77.056 2.428 79.594 offTargetAnalysisWithoutBSgenome 10.771 0.171 10.946 offTargetAnalysis 6.296 0.145 6.446 * 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.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CRISPRseek’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CRISPRseek)
CRISPRseek.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #BiocGenerics:::testPackage("CRISPRseek") > > proc.time() user system elapsed 0.070 0.019 0.086
CRISPRseek.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS="") > require("CRISPRseek") || stop("unable to load Package:CRISPRseek") Loading required package: CRISPRseek Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit [1] TRUE > require("BSgenome.Hsapiens.UCSC.hg19") || + stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19") Loading required package: 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 [1] TRUE > require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db") Loading required package: org.Hs.eg.db 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")'. [1] TRUE > require("TxDb.Hsapiens.UCSC.hg19.knownGene") || + stop("unable to load TxDb.Hsapiens.UCSC.hg19.knownGene") Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene Loading required package: GenomicFeatures [1] TRUE > require("BSgenome.Mmusculus.UCSC.mm10") || + stop("unable to load Package: BSgenome.Mmusculus.UCSC.mm10") Loading required package: BSgenome.Mmusculus.UCSC.mm10 [1] TRUE > require("TxDb.Mmusculus.UCSC.mm10.knownGene") || + stop("unable to load Package:TxDb.Mmusculus.UCSC.mm10.knownGene") Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene [1] TRUE > require("org.Mm.eg.db") || + stop("unable to load Package:org.Mm.eg.db") Loading required package: org.Mm.eg.db [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("CRISPRseek") testing compare2Sequences search for gRNAs for input file1... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Aug-26-2024/ search for gRNAs for input file2... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Aug-26-2024/ [1] "Scoring ..." >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 2 >>> Finding all hits in sequence rs362331T ... >>> DONE searching finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" search for gRNAs for input file1... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Aug-26-2024/ search for gRNAs for input file2... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Aug-26-2024/ [1] "Scoring ..." >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 2 >>> Finding all hits in sequence rs362331T ... >>> DONE searching finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" search for gRNAs for input file1... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331T.fa-Aug-26-2024/ search for gRNAs for input file2... Validating input ... Searching for gRNAs ... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/rs362331C.fa-Aug-26-2024/ [1] "Scoring ..." >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 2 >>> Finding all hits in sequence rs362331T ... >>> DONE searching finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" search for gRNAs for input file1... [1] "Scoring ..." >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" [1] "Scoring ..." finish off-target search in sequence 2 >>> Finding all hits in sequence rs362331C ... >>> DONE searching finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" testing gRNAs provided and filter gRNAs with RE for offTargetAnalysis Validating input ... >>> Finding all hits in sequence chr4 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Validating input ... >>> Finding all hits in sequence chr4 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Validating input ... >>> Finding all hits in sequence chr4 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Validating input ... >>> Finding all hits in sequence chr4 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ testing gRNAs provided without filtering gRNAs with RE for offTargetAnalysis checking N in PAM...Testing for mouse with orgAnn... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for mouse without orgAnn... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for mouse without orgAnn... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for findgRNAs = FALSE... Validating input ... >>> Finding all hits in sequence chr3 ... >>> DONE searching >>> Finding all hits in sequence chr4 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr6 ... >>> DONE searching >>> Finding all hits in sequence chr8 ... >>> DONE searching >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr15 ... >>> DONE searching >>> Finding all hits in sequence chrX ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Scan for REsites in flanking region... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr2 ... >>> DONE searching >>> Finding all hits in sequence chr3 ... >>> DONE searching >>> Finding all hits in sequence chr4 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr6 ... >>> DONE searching >>> Finding all hits in sequence chr7 ... >>> DONE searching >>> Finding all hits in sequence chr8 ... >>> DONE searching >>> Finding all hits in sequence chr9 ... >>> DONE searching >>> Finding all hits in sequence chr10 ... >>> DONE searching >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr12 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> DONE searching >>> Finding all hits in sequence chr14 ... >>> DONE searching >>> Finding all hits in sequence chr15 ... >>> DONE searching >>> Finding all hits in sequence chr16 ... >>> DONE searching >>> Finding all hits in sequence chr17 ... >>> DONE searching >>> Finding all hits in sequence chr18 ... >>> DONE searching >>> Finding all hits in sequence chr19 ... >>> DONE searching >>> Finding all hits in sequence chr20 ... >>> DONE searching >>> Finding all hits in sequence chr22 ... >>> DONE searching >>> Finding all hits in sequence chrX ... >>> DONE searching >>> Finding all hits in sequence chrY ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for paired with RE sites... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr2 ... >>> DONE searching >>> Finding all hits in sequence chr3 ... >>> DONE searching >>> Finding all hits in sequence chr4 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr6 ... >>> DONE searching >>> Finding all hits in sequence chr7 ... >>> DONE searching >>> Finding all hits in sequence chr8 ... >>> DONE searching >>> Finding all hits in sequence chr9 ... >>> DONE searching >>> Finding all hits in sequence chr10 ... >>> DONE searching >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr12 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> DONE searching >>> Finding all hits in sequence chr14 ... >>> DONE searching >>> Finding all hits in sequence chr15 ... >>> DONE searching >>> Finding all hits in sequence chr16 ... >>> DONE searching >>> Finding all hits in sequence chr17 ... >>> DONE searching >>> Finding all hits in sequence chr18 ... >>> DONE searching >>> Finding all hits in sequence chr19 ... >>> DONE searching >>> Finding all hits in sequence chr20 ... >>> DONE searching >>> Finding all hits in sequence chr22 ... >>> DONE searching >>> Finding all hits in sequence chrX ... >>> DONE searching >>> Finding all hits in sequence chrY ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for paired with or without RE sites... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr2 ... >>> DONE searching >>> Finding all hits in sequence chr3 ... >>> DONE searching >>> Finding all hits in sequence chr4 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr6 ... >>> DONE searching >>> Finding all hits in sequence chr7 ... >>> DONE searching >>> Finding all hits in sequence chr8 ... >>> DONE searching >>> Finding all hits in sequence chr9 ... >>> DONE searching >>> Finding all hits in sequence chr10 ... >>> DONE searching >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr12 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> DONE searching >>> Finding all hits in sequence chr14 ... >>> DONE searching >>> Finding all hits in sequence chr15 ... >>> DONE searching >>> Finding all hits in sequence chr16 ... >>> DONE searching >>> Finding all hits in sequence chr17 ... >>> DONE searching >>> Finding all hits in sequence chr18 ... >>> DONE searching >>> Finding all hits in sequence chr19 ... >>> DONE searching >>> Finding all hits in sequence chr20 ... >>> DONE searching >>> Finding all hits in sequence chr22 ... >>> DONE searching >>> Finding all hits in sequence chrX ... >>> DONE searching >>> Finding all hits in sequence chrY ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for unPaired with RE sites... Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr1 ... >>> DONE searching >>> Finding all hits in sequence chr2 ... >>> DONE searching >>> Finding all hits in sequence chr3 ... >>> DONE searching >>> Finding all hits in sequence chr4 ... >>> DONE searching >>> Finding all hits in sequence chr5 ... >>> DONE searching >>> Finding all hits in sequence chr6 ... >>> DONE searching >>> Finding all hits in sequence chr7 ... >>> DONE searching >>> Finding all hits in sequence chr8 ... >>> DONE searching >>> Finding all hits in sequence chr9 ... >>> DONE searching >>> Finding all hits in sequence chr10 ... >>> DONE searching >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr12 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> DONE searching >>> Finding all hits in sequence chr14 ... >>> DONE searching >>> Finding all hits in sequence chr15 ... >>> DONE searching >>> Finding all hits in sequence chr16 ... >>> DONE searching >>> Finding all hits in sequence chr17 ... >>> DONE searching >>> Finding all hits in sequence chr18 ... >>> DONE searching >>> Finding all hits in sequence chr19 ... >>> DONE searching >>> Finding all hits in sequence chr20 ... >>> DONE searching >>> Finding all hits in sequence chr22 ... >>> DONE searching >>> Finding all hits in sequence chrX ... >>> DONE searching >>> Finding all hits in sequence chrY ... >>> 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 /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for unPaired with or without RE sites... Testing for target not found when a gRNA sequence is from another species serving as a negative control… Validating input ... >>> Finding all hits in sequence chr11 ... >>> DONE searching >>> Finding all hits in sequence chr12 ... >>> DONE searching >>> Finding all hits in sequence chr13 ... >>> DONE searching >>> Finding all hits in sequence chr18 ... >>> DONE searching >>> Finding all hits in sequence chr19 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ Testing for target and offtarget not found when a gRNAsequence is from another species serving as a negative control… Validating input ... >>> Finding all hits in sequence chr12 ... >>> DONE searching Testing for 5 prime PAM target and offtarget not found when qgRNA sequence is from another species serving as a negative control… Validating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr12 ... >>> DONE searching 2nd testValidating input ... Searching for gRNAs ... >>> Finding all hits in sequence chr12 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... Annotating, filtering and generating reports ... Done annotating Add RE information... write gRNAs to bed file... Done. Please check output files in directory /Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck/tests/testthat/ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ] > > proc.time() user system elapsed 571.883 8.251 580.357
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
name | user | system | elapsed | |
CRISPRseek-package | 77.056 | 2.428 | 79.594 | |
annotateOffTargets | 1.254 | 0.042 | 1.300 | |
buildFeatureVectorForScoring | 0.022 | 0.001 | 0.023 | |
calculategRNAEfficiency | 0.004 | 0.003 | 0.010 | |
compare2Sequences | 2.207 | 0.085 | 2.306 | |
deepCpf1 | 0.020 | 0.001 | 0.022 | |
filterOffTarget | 1.348 | 0.055 | 1.405 | |
filtergRNAs | 0.167 | 0.008 | 0.175 | |
findgRNAs | 0.080 | 0.003 | 0.084 | |
getOfftargetScore | 0.024 | 0.001 | 0.024 | |
isPatternUnique | 0.004 | 0.000 | 0.004 | |
offTargetAnalysis | 6.296 | 0.145 | 6.446 | |
offTargetAnalysisWithoutBSgenome | 10.771 | 0.171 | 10.946 | |
predictRelativeFreqIndels | 0 | 0 | 0 | |
searchHits | 0.038 | 0.002 | 0.041 | |
searchHits2 | 1.589 | 0.103 | 1.691 | |
translatePattern | 0.001 | 0.000 | 0.000 | |
uniqueREs | 0.100 | 0.003 | 0.103 | |
writeHits | 0 | 0 | 0 | |
writeHits2 | 0.044 | 0.003 | 0.047 | |