Lihua Julie Zhu
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/CRISPRseek |
| git_branch: RELEASE_3_20 |
| git_last_commit: 8f7dfec |
| git_last_commit_date: 2024-10-29 09:49:23 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:07 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 459/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.46.0 (landing page) Lihua Julie Zhu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | TIMEOUT | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.46.0 |
| 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_1.46.0.tar.gz |
| StartedAt: 2025-01-03 01:41:01 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 02:21:01 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: CRISPRseek.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_1.46.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ... 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 206.433 9.536 1594.408
offTargetAnalysisWithoutBSgenome 85.592 0.935 101.487
offTargetAnalysis 22.466 0.451 26.271
compare2Sequences 17.102 0.344 21.841
filterOffTarget 7.342 0.247 8.438
annotateOffTargets 6.646 0.272 7.381
searchHits2 4.600 0.177 5.754
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘testthat.R’
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-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
0.356 0.122 0.461
CRISPRseek.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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, saveRDS, 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-Jan-03-2025/
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-Jan-03-2025/
[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-Jan-03-2025/
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-Jan-03-2025/
[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-Jan-03-2025/
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-Jan-03-2025/
[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 ...
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 206.433 | 9.536 | 1594.408 | |
| annotateOffTargets | 6.646 | 0.272 | 7.381 | |
| buildFeatureVectorForScoring | 0.272 | 0.053 | 0.337 | |
| calculategRNAEfficiency | 0.031 | 0.011 | 0.046 | |
| compare2Sequences | 17.102 | 0.344 | 21.841 | |
| deepCpf1 | 0.100 | 0.005 | 0.137 | |
| filterOffTarget | 7.342 | 0.247 | 8.438 | |
| filtergRNAs | 1.391 | 0.011 | 2.098 | |
| findgRNAs | 0.636 | 0.020 | 0.980 | |
| getOfftargetScore | 0.210 | 0.005 | 0.222 | |
| isPatternUnique | 0.029 | 0.001 | 0.030 | |
| offTargetAnalysis | 22.466 | 0.451 | 26.271 | |
| offTargetAnalysisWithoutBSgenome | 85.592 | 0.935 | 101.487 | |
| predictRelativeFreqIndels | 0.000 | 0.001 | 0.001 | |
| searchHits | 0.345 | 0.012 | 0.494 | |
| searchHits2 | 4.600 | 0.177 | 5.754 | |
| translatePattern | 0.000 | 0.001 | 0.002 | |
| uniqueREs | 0.797 | 0.018 | 0.914 | |
| writeHits | 0.001 | 0.001 | 0.003 | |
| writeHits2 | 0.336 | 0.018 | 0.382 | |